Genetically modified non-human animal with human or chimeric cd40

ABSTRACT

The present disclosure relates to genetically modified non-human animals that express a human or chimeric (e.g., humanized) CD40, and methods of use thereof.

CLAIM OF PRIORITY

This application is a continuation of and claims priority to international Application No. PCT/CN2018/091845, filed on Jun. 19, 2018, which claims the benefit of Chinese Patent Application App. No. 201710464564.4, filed on Jun. 19, 2017, Chinese Patent Application App. No. 201710872886.2, filed on Sep. 25, 2017, and Chinese Patent Application App. No. 201810622839.7 filed on Jun. 15, 2018. The entire contents of the foregoing are incorporated herein by reference.

TECHNICAL FIELD

This disclosure relates to genetically modified animal expressing human or chimeric (e.g., humanized) CD40, and methods of use thereof.

BACKGROUND

The immune system has developed multiple mechanisms to prevent deleterious activation of immune cells. One such mechanism is the intricate balance between positive and negative costimulatory signals delivered to immune cells. Targeting the stimulatory or inhibitory pathways for the immune system is considered to be a potential approach for the treatment of various diseases, e.g., cancers and autoimmune diseases.

The traditional drug research and development for these stimulatory or inhibitory receptors typically use in vitro screening approaches. However, these screening approaches cannot provide the body environment (such as tumor microenvironment, stromal cells, extracellular matrix components and immune cell interaction, etc.), resulting in a higher rate of failure in drug development. In addition, in view of the differences between humans and animals, the test results obtained from the use of conventional experimental animals for in vivo pharmacological test may not reflect the real disease state and the interaction at the targeting sites, resulting in that the results in many clinical trials are significantly different from the animal experimental results. Therefore, the development of humanized animal models that are suitable for human antibody screening and evaluation will significantly improve the efficiency of new drug development and reduce the cost for drug research and development.

SUMMARY

This disclosure is related to an animal model with human CD40 or chimeric CD40. The animal model can express human CD40 or chimeric CD40 (e.g., humanized CD40) protein in its body. It can be used in the studies on the function of CD40 gene, and can be used in the screening and evaluation of anti-human CD40 antibodies. In addition, the animal models prepared by the methods described herein can be used in drug screening, pharmacodynamics studies, treatments for immune-related diseases (e.g., autoimmune disease), and cancer therapy for human CD40 target sites; they can also be used to facilitate the development and design of new drugs, and save time and cost. In summary, this disclosure provides a powerful tool for studying the function of CD40 protein and a platform for screening cancer drugs.

In one aspect, the disclosure relates to genetically-modified, non-human animals whose genome comprises at least one chromosome comprising a sequence encoding a human or chimeric CD40. In some embodiments, the sequence encoding the human or chimeric CD40 is operably linked to an endogenous regulatory element at the endogenous CD40 gene locus in the at least one chromosome. In some embodiments, the sequence encoding a human or chimeric CD40 comprises a sequence encoding an amino acid sequence that is at least 50%, 55%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% identical to human CD40 (NP_001241.1 (SEQ ID NO: 23)). In some embodiments, the sequence encoding a human or chimeric CD40 comprises a sequence encoding an amino acid sequence that is at least 50%, 55%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% identical to SEQ ID NO: 27. In some embodiments, the sequence encoding a human or chimeric CD40 comprises a sequence encoding an amino acid sequence that corresponds to amino acids 20-192 of SEQ ID NO: 23.

In some embodiments, the animal is a mammal, e.g., a monkey, a rodent or a mouse. In some embodiments, the animal is a C57BL/6 mouse. In some embodiments, the animal does not express endogenous CD40. In some embodiments, the animal has one or more cells expressing human or chimeric CD40. In some embodiments, the expressed human or chimeric CD40 can bind to or interact with human protein CD40L (also known as CD154). In some embodiments, the expressed human or chimeric CD40 can bind to or interact with endogenous CD154.

In one aspect, the disclosure relates to genetically-modified, non-human animals, wherein the genome of the animals comprises a replacement, at an endogenous CD40 gene locus, of a sequence encoding a region of endogenous CD40 with a sequence encoding a corresponding region of human CD40. In some embodiments, the sequence encoding the corresponding region of human CD40 is operably linked to an endogenous regulatory element at the endogenous CD40 locus, and one or more cells of the animal expresses a chimeric CD40. In some embodiments, the animal does not express endogenous CD40. In some embodiments, the locus of endogenous CD40 is the extracellular region of CD40. In some embodiments, the animal has one or more cells expressing a chimeric CD40 having an extracellular region, a transmembrane region, and a cytoplasmic region, wherein the extracellular region comprises a sequence that is at least 50%, 60%, 70%, 80%, 90%, 95%, or 99% identical to the extracellular region of human CD40. In some embodiments, the extracellular region of the chimeric CD40 has a sequence that has at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, or 180 contiguous amino acids that are identical to a contiguous sequence present in the extracellular region of human CD40. In some embodiments, the animal is a mouse, and the sequence encoding the region of endogenous CD40 is exon 2, exon 3, exon 4, exon 5, exon 6, and/or exon 7 of the endogenous mouse CD40 gene. In some embodiments, the animal is heterozygous with respect to the replacement at the endogenous CD40 gene locus. In some embodiments, the animal is homozygous with respect to the replacement at the endogenous CD40 gene locus.

In one aspect, the disclosure relates to methods for making a genetically-modified, non-human animal. The methods involve replacing in at least one cell of the animal, at an endogenous CD40 gene locus, a sequence encoding a region of an endogenous CD40 with a sequence encoding a corresponding region of human CD40. In some embodiments, the sequence encoding the corresponding region of human CD40 comprises exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, and/or exon 9 of a human CD40 gene. In some embodiments, the sequence encoding the corresponding region of CD40 comprises exon 2, exon 3, exon 4, exon 5, exon 6, and/or exon 7 (or part thereof, e.g., part of exon 2 and/or exon 7) of a human CD40 gene. In some embodiments, the sequence encoding the corresponding region of human CD40 encodes amino acids 20-192 of SEQ ID NO: 23. In some embodiments, the region is located within the extracellular region of CD40. In some embodiments, the animal is a mouse, and the sequence encoding the region of the endogenous CD40 locus is exon 2, exon 3, exon 4, exon 5, exon 6, and/or exon 7 of mouse CD40 gene (e.g., part of exon 2, exon 3, exon 4, exon 5, exon 6, and part of exon 7).

In one aspect, the disclosure relates to non-human animals comprising at least one cell comprising a nucleotide sequence encoding a chimeric CD40 polypeptide, wherein the chimeric CD40 polypeptide comprises at least 50 contiguous amino acid residues that are identical to the corresponding contiguous amino acid sequence of a human CD40, wherein the animal expresses the chimeric CD40. In some embodiments, the chimeric CD40 polypeptide has at least 50 contiguous amino acid residues that are identical to the corresponding contiguous amino acid sequence of a human CD40 extracellular region. In some embodiments, the chimeric CD40 polypeptide comprises a sequence that is at least 90%, 95%, or 99% identical to amino acids 20-192 of SEQ ID NO: 23. In some embodiments, the nucleotide sequence is operably linked to an endogenous CD40 regulatory element of the animal. In some embodiments, the chimeric CD40 polypeptide comprises an endogenous CD40 transmembrane region and/or an endogenous CD40 cytoplasmic region. In some embodiments, the nucleotide sequence is integrated to an endogenous CD40 gene locus of the animal. In some embodiments, the chimeric CD40 has at least one mouse CD40 activity (e.g., interacting with mouse CD154, and promoting immune responses in mice) and/or at least one human CD40 activity (e.g., interacting with human CD154, and promoting immune responses in human).

In one aspect, the disclosure relates to methods of making a genetically-modified mouse cell that expresses a chimeric CD40, the method including: replacing, at an endogenous mouse CD40 gene locus, a nucleotide sequence encoding a region of mouse CD40 with a nucleotide sequence encoding a corresponding region of human CD40, thereby generating a genetically-modified mouse cell that includes a nucleotide sequence that encodes the chimeric CD40, wherein the mouse cell expresses the chimeric CD40. In some embodiments, the chimeric CD40 comprises a signal peptide sequence (e.g., a mouse signal peptide sequence or a human signal peptide sequence), an extracellular region of mouse CD40, an extracellular region of human CD40, a transmembrane and/or a cytoplasmic region of a mouse CD40. In some embodiments, the nucleotide sequence encoding the chimeric CD40 is operably linked to an endogenous CD40 regulatory region, e.g., promoter.

In some embodiments, the animals further comprise a sequence encoding an additional human or chimeric protein. In some embodiments, the additional human or chimeric protein is programmed cell death protein 1 (PD-1), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), Lymphocyte Activating 3 (LAG-3), B And T Lymphocyte Associated (BTLA), Programmed Cell Death 1 Ligand 1 (PD-L1), CD27, CD28, CD47, CD137, CD154, T-Cell Immunoreceptor With Ig And ITIM Domains (TIGIT), Glucocorticoid-Induced TNFR-Related Protein (GITR), T-cell immunoglobulin and mucin-domain containing-3 (TIM-3), Signal regulatory protein α (SIRPα) or TNF Receptor Superfamily Member 4 (TNFRSF4 or OX40).

In one aspect, the disclosure relates to methods of determining effectiveness of an anti-CD40 antibody for the treatment of cancer, including: administering the anti-CD40 antibody to the animal as described herein, wherein the animal has a tumor, and determining the inhibitory effects of the anti-CD40 antibody to the tumor. In some embodiments, the animal has one or more cells (e.g., antigen presenting cells (APC)) that express CD40. In some embodiments, the animal has one or more tumor cells that express CD40.

In some embodiments, the tumor comprises one or more cancer cells that are injected into the animal. In some embodiments, determining the inhibitory effects of the anti-CD40 antibody to the tumor involves measuring the tumor volume in the animal. In some embodiments, the tumor cells are melanoma cells (e.g., advanced melanoma cells), non-small cell lung carcinoma (NSCLC) cells, small cell lung cancer (SCLC) cells, bladder cancer cells, non-Hodgkin lymphoma cells, and/or prostate cancer cells (e.g., metastatic hormone-refractory prostate cancer). In some embodiments, the tumor cells are hepatocellular, ovarian, colon, or cervical tumor cells. In some embodiments, the tumor cells are breast cancer cells, ovarian cancer cells, and/or solid tumor cells. In some embodiments, the tumor cells are lymphoma cells, colorectal cancer cells, or oropharyngeal cancer cells. In some embodiments, the animal has metastatic solid tumors, NSCLC, melanoma, lymphoma (e.g., non-Hodgkin lymphoma), colorectal cancer, or multiple myeloma. In some embodiments, the animal has melanoma, pancreatic carcinoma, mesothelioma, hematological malignancies (e.g., Non-Hodgkin's lymphoma, lymphoma, chronic lymphocytic leukemia), or solid tumors.

In one aspect, the disclosure relates to methods of determining effectiveness of an anti-CD40 antibody for the treatment of various immune-related disorders, e.g., autoimmune diseases.

In one aspect, the disclosure relates to methods of determining effectiveness of an anti-CD40 antibody and an additional therapeutic agent for the treatment of a tumor, including administering the anti-CD40 antibody and the additional therapeutic agent to the animal as described herein, wherein the animal has a tumor, and determining the inhibitory effects on the tumor. In some embodiments, the animal or mouse further comprises a sequence encoding an additional human or chimeric protein. In some embodiments, the additional human or chimeric protein is PD-1, CTLA-4, LAG-3, BTLA, PD-L1, CD27, CD28, CD47, CD137, CD154, TIGIT, TIM-3, GITR, SIRPα or OX40. In some embodiments, the animal further comprises a sequence encoding a human or chimeric PD-1, PD-L1, or CTLA-4.

In some embodiments, the additional therapeutic agent is an antibody (e.g., human antibody) the specifically binds to PD-1, CTLA-4, LAG-3, BTLA, PD-L1, CD27, CD28, CD47, CD137, CD154, TIGIT, TIM-3, GITR, SIRPα, OX40, CD20, EGFR, or CD319. In some embodiments, the additional therapeutic agent is an anti-PD-1 antibody (e.g., nivolumab), an anti-PD-L1 antibody, an anti-CTLA4 antibody (e.g., ipilimumab), an anti-CD20 antibody (e.g., rituximab), an anti-EGFR antibody (e.g., cetuximab), or an anti-CD319 antibody (e.g., elotuzumab).

In some embodiments, the animal comprises one or more cells (e.g., antigen presenting cells, B cells, macrophages, dendritic cells, or tumor cells) that express CD40. In some embodiments, the animal comprises one or more cells (e.g., T cells) that express CD154. In some embodiments, the tumor comprises one or more tumor cells that express CD40. In some embodiments, the tumor comprises one or more tumor cells that express PD-L1, PD-L2, CD80 or CD86. In some embodiments, the tumor is caused by injection of one or more cancer cells into the animal. In some embodiments, determining the inhibitory effects of the treatment involves measuring the tumor volume in the animal. In some embodiments, the tumor comprises melanoma cells, non-small cell lung carcinoma (NSCLC) cells, small cell lung cancer (SCLC) cells, bladder cancer cells, and/or prostate cancer cells (e.g., metastatic hormone-refractory prostate cancer cells). In some embodiments, the animal has metastatic solid tumors, NSCLC, melanoma, lymphoma (e.g., non-Hodgkin lymphoma), colorectal cancer, or multiple myeloma. In some embodiments, the animal has melanoma, pancreatic carcinoma, mesothelioma, hematological malignancies (e.g., Non-Hodgkin's lymphoma, lymphoma, chronic lymphocytic leukemia), or solid tumors.

In one aspect, the disclosure relates to proteins comprising an amino acid sequence, wherein the amino acid sequence is one of the following: (a) an amino acid sequence set forth in SEQ ID NO: 27; (b) an amino acid sequence that is at least 90% identical to SEQ ID NO: 27; (c) an amino acid sequence that is at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 27; (d) an amino acid sequence that is different from the amino acid sequence set forth in SEQ ID NO: 27 by no more than 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 amino acid; and (e) an amino acid sequence that comprises a substitution, a deletion and/or insertion of one, two, three, four, five or more amino acids to the amino acid sequence set forth in SEQ ID NO: 27. In some embodiments, provided herein are cells comprising the proteins disclosed herein. In some embodiments, provided herein are animals having the proteins disclosed herein.

In one aspect, the disclosure relates to nucleic acids comprising a nucleotide sequence, wherein the nucleotide sequence is one of the following: (a) a sequence that encodes the protein as described herein; (b) SEQ ID NO: 25; (c) SEQ ID NO: 26; (d) a sequence that is at least 90% identical to SEQ ID NO: 25 or SEQ ID NO: 26; (e) a sequence that is at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 25; and (f) a sequence that is at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 26. In some embodiments, provided herein are cells comprising the nucleic acids disclosed herein. In some embodiments, provided herein are animals having the nucleic acids disclosed herein.

In another aspect, the disclosure also provides a genetically-modified, non-human animal whose genome comprise a disruption in the animal's endogenous CD40 gene, wherein the disruption of the endogenous CD40 gene comprises deletion of exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, and/or exon 9, or part thereof of the endogenous CD40 gene.

In some embodiments, the disruption of the endogenous CD40 gene comprises deletion of one or more exons or part of exons selected from the group consisting of exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, and exon 9 of the endogenous CD40 gene.

In some embodiments, the disruption of the endogenous CD40 gene further comprises deletion of one or more introns or part of introns selected from the group consisting of intron 1, intron 2, intron 3, intron 4, intron 5, intron 6, intron 7, and intron 8 of the endogenous CD40 gene.

In some embodiments, wherein the deletion can comprise deleting at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 10, 220, 230, 240, 250, 260, 270, 280, 290, 300, 350, 400, 450, 500, 550, 600, 650, or more nucleotides.

In some embodiments, the disruption of the endogenous CD40 gene comprises the deletion of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 10, 220, 230, 240, 250, 260, 270, 280, 290, or 300 nucleotides of exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, and/or exon 9 (e.g., deletion of at least 300 nucleotides of exon 2 or exon 7).

In some embodiments, the mice described in the present disclosure can be mated with the mice containing other human or chimeric genes (e.g., chimeric SIRPα, chimeric PD-1, chimeric PD-L1, chimeric CTLA-4, or other immunomodulatory factors), so as to obtain a mouse expressing two or more human or chimeric proteins. The mice can also, e.g., be used for screening antibodies in the case of a combined use of drugs, as well as evaluating the efficacy of the combination therapy.

In another aspect, the disclosure further provides methods of determining toxicity of an agent (e.g., a CD40 antagonist or agonist). The methods involve administering the agent to the animal as described herein; and determining weight change of the animal. In some embodiments, the method further involve performing a blood test (e.g., determining red blood cell count).

In one aspect, the disclosure relates to a targeting vector, including a) a DNA fragment homologous to the 5′ end of a region to be altered (5′ arm), which is selected from the CD40 gene genomic DNAs in the length of 100 to 10,000 nucleotides; b) a desired/donor DNA sequence encoding a donor region; and c) a second DNA fragment homologous to the 3′ end of the region to be altered (3′ arm), which is selected from the CD40 gene genomic DNAs in the length of 100 to 10,000 nucleotides.

In some embodiments, a) the DNA fragment homologous to the 5′ end of a region to be altered (5′ arm/receptor) is selected from the nucleotide sequences that have at least 90% homology to the NCBI accession number NC_000068.7; c) the DNA fragment homologous to the 3′ end of the region to be altered (3′ arm/receptor) is selected from the nucleotide sequences that have at least 90% homology to the NCBI accession number NC_000068.7.

In some embodiments, a) the DNA fragment homologous to the 5′ end of a region to be altered (5′ arm/receptor) is selected from the nucleotides from the position 165060750 to the position 165062291 of the NCBI accession number NC_000068.7; c) the DNA fragment homologous to the 3′ end of the region to be altered (3′ arm/receptor) is selected from the nucleotides from the position 165069646 to the position 165071120 of the NCBI accession number NC_000068.7.

In some embodiments, a length of the selected genomic nucleotide sequence is more than 3 kb, 3.5 kb, 4 kb, 4.5 kb, 5 kb, 5.5 kb, or 6 kb. In some embodiments, the length is about 6329 bp. In some embodiments, the region to be altered is exon 2, exon 3, exon 4, exon 5, exon 6, and/or exon 7 of mouse CD40 gene.

In some embodiments, the sequence of the 5′ arm is shown in SEQ ID NO: 28. In some embodiments, the sequence of the 3′ arm is shown in SEQ ID NO: 29.

In some embodiments, the targeting vector further includes a selectable gene marker.

In some embodiments, the target region is derived from human. In some embodiments, the target region is a part or entirety of the nucleotide sequence of a humanized CD40. In some embodiments, the nucleotide sequence is shown as one or more of exon 2, exon 3, exon 4, exon 5, exon 6, and exon 7 of the human CD40.

In some embodiments, the nucleotide sequence of the human CD40 encodes the human CD40 protein with the NCBI accession number NP_001241.1 (SEQ ID NO: 23). In some emboldens, the nucleotide sequence of the human CD40 is selected from the nucleotides from the position 46121826 to the position 46128154 of NC_000020.11 (SEQ ID NO: 30).

The disclosure also relates to a cell including the targeting vector as described herein.

The disclosure also relates to a method for establishing a genetically-modified non-human animal expressing two human or chimeric (e.g., humanized) genes. The method includes the steps of

(a) using the method for establishing a CD40 gene humanized animal model to obtain a CD40 gene genetically modified humanized mouse;

(b) mating the CD40 gene genetically modified humanized mouse obtained in step (a) with another humanized mouse, and then screening to obtain a double humanized mouse model.

In some embodiments, in step (b), the CD40 gene genetically modified humanized mouse obtained in step (a) is mated with a PD-1 or PD-L1 humanized mouse to obtain a CD40 and PD-1 double humanized mouse model or a CD40 and PD-L1 double humanized mouse model.

The disclosure also relates to non-human mammal generated through the methods as described herein.

In some embodiments, the genome thereof contains human gene(s).

In some embodiments, the non-human mammal is a rodent. In some embodiments, the non-human mammal is a mouse.

In some embodiments, the non-human mammal expresses a protein encoded by a humanized CD40 gene.

The disclosure also relates to an offspring of the non-human mammal.

In another aspect, the disclosure relates to a tumor bearing non-human mammal model, characterized in that the non-human mammal model is obtained through the methods as described herein.

In some embodiments, the non-human mammal is a rodent. In some embodiments, the non-human mammal is a mouse.

The disclosure also relates to a cell (e.g., stem cell or embryonic stem cell) or cell line, or a primary cell culture thereof derived from the non-human mammal or an offspring thereof, or the tumor bearing non-human mammal.

The disclosure further relates to the tissue, organ or a culture thereof derived from the non-human mammal or an offspring thereof, or the tumor bearing non-human mammal.

In another aspect, the disclosure relates to a tumor tissue derived from the non-human mammal or an offspring thereof when it bears a tumor, or the tumor bearing non-human mammal.

In one aspect, the disclosure relates to a CD40 amino acid sequence of a humanized mouse, wherein the amino acid sequence is selected from the group consisting of:

a) an amino acid sequence shown in SEQ ID NO: 27;

b) an amino acid sequence having a homology of at least 90% with the amino acid sequence shown in SEQ ID NO: 27;

c) an amino acid sequence encoded by a nucleic acid sequence, wherein the nucleic acid sequence is able to hybridize to a nucleotide sequence encoding the amino acid shown in SEQ ID NO: 27 under a low stringency condition or a strict stringency condition;

d) an amino acid sequence having a homology of at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% with the amino acid sequence shown in SEQ ID NO: 27;

e) an amino acid sequence that is different from the amino acid sequence shown in SEQ ID NO: 27 by no more than 10, 9, 8, 7, 6, 5, 4, 3, 2 or no more than 1 amino acid;

or

f) an amino acid sequence that comprises a substitution, a deletion and/or insertion of one or more amino acids to the amino acid sequence shown in SEQ ID NO: 27.

The disclosure also relates to a CD40 nucleic acid sequence of a humanized mouse, wherein the nucleic acid sequence is selected from the group consisting of:

a) a nucleic acid sequence that encodes the CD40 amino acid sequence of a humanized mouse;

b) a nucleic acid sequence that is set forth in SEQ ID NO: 25 or SEQ ID NO: 26;

c) a nucleic acid sequence that can hybridize to the nucleotide sequence as shown in SEQ ID NO: 25 or SEQ ID NO: 26 under a low stringency condition or a strict stringency condition;

d) a nucleic acid sequence that has a homology of at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% with the nucleotide sequence as shown in SEQ ID NO: 25 or SEQ ID NO: 26;

f) a nucleic acid sequence that encodes an amino acid sequence, wherein the amino acid sequence has a homology of at least 90% with the amino acid sequence shown in SEQ ID NO: 27;

g) a nucleic acid sequence that encodes an amino acid sequence, wherein the amino acid sequence has a homology of at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% with the amino acid sequence shown in SEQ ID NO: 27;

h) a nucleic acid sequence that encodes an amino acid sequence, wherein the amino acid sequence is different from the amino acid sequence shown in SEQ ID NO: 27 by no more than 10, 9, 8, 7, 6, 5, 4, 3, 2 or no more than 1 amino acid; and/or

i) a nucleic acid sequence that encodes an amino acid sequence, wherein the amino acid sequence comprises a substitution, a deletion and/or insertion of 1, 2, 3, 4, 5, 6, 7, 8, 9, or more amino acids to the amino acid sequence shown in SEQ ID NO: 27.

The disclosure further relates to a CD40 genomic DNA sequence of a humanized mouse, a DNA sequence obtained by a reverse transcription of the mRNA obtained by transcription thereof is consistent with or complementary to the DNA sequence; a construct expressing the amino acid sequence thereof; a cell comprising the construct thereof; a tissue comprising the cell thereof.

The disclosure further relates to the use of the non-human mammal or an offspring thereof, or the tumor bearing non-human mammal, the animal model generated through the method as described herein in the development of a product related to an immunization processes of human cells, the manufacture of a human antibody, or the model system for a research in pharmacology, immunology, microbiology and medicine.

The disclosure also relates to the use of the non-human mammal or an offspring thereof, or the tumor bearing non-human mammal, the animal model generated through the method as described herein in the production and utilization of an animal experimental disease model of an immunization processes involving human cells, the study on a pathogen, or the development of a new diagnostic strategy and/or a therapeutic strategy.

The disclosure further relates to the use of the non-human mammal or an offspring thereof, or the tumor bearing non-human mammal, the animal model generated through the methods as described herein, in the screening, verifying, evaluating or studying the CD40 gene function, human CD40 antibodies, the drugs or efficacies for human CD40 targeting sites, and the drugs for immune-related diseases and antitumor drugs.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Methods and materials are described herein for use in the present invention; other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.

Other features and advantages of the invention will be apparent from the following detailed description and figures, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1A is a graph showing activity testing results for sgRNA1-sgRNA7 (Con is a negative control; PC is a positive control).

FIG. 1B is a graph showing activity testing results for sgRNA8-sgRNA14 (Con is a negative control; PC is a positive control).

FIG. 2 is a schematic diagram showing the structure of pT7-sgRNA-G2 plasmid.

FIG. 3 is a schematic diagram showing a gene targeting strategy.

FIG. 4 is a schematic diagram showing a map of an example of humanized CD40 gene in mouse.

FIG. 5 shows the restriction enzymes digestion results of the targeting plasmid pClon-2G-CD40 by three sets of restriction enzymes.

FIGS. 6A-6B show PCR identification results of samples collected from tails of F0 generation mice. WT is wildtype; + is positive control. Mice labeled with F0-1 and F0-2 are positive.

FIG. 7 is flow cytometry results of wildtype mice and heterozygous humanized CD40 mice. Anti-mCD3 antibody was used to activate spleen cells. Flow cytometry was performed with 1) antibody against mouse CD40 (mCD40PE) and antibody against mouse CD19 (mCD19 FITC); and 2) antibody against human CD40 (hCD40 APC), and antibody against mouse CD19 (mCD19 FITC). In the control groups, spleen cells that express human or humanized CD40 were not detected. Humanized CD40 was detected on spleen cells in heterozygous humanized CD40 mice.

FIGS. 8A-8F are flow cytometry results of wildtype mice (FIGS. 8A, 8B, 8D, and 8E) and humanized CD40 homozygous mice (FIGS. 8C, 8F). CD3 antibody was used to activate spleen cells in FIGS. 8B, 8C, 8E and 8F. Flow cytometry was performed with 1) antibody against mouse CD40 (mCD40PE) and antibody against mouse CD19 (mCD19 FITC) (FIGS. 8A-8C); and 2) antibody against human CD40 (hCD40 APC), and antibody against mouse CD19 (mCD19 FITC) (FIGS. 8D-8F). In the control groups, spleen cells that express human or humanized CD40 were not detected. Humanized CD40 was detected on spleen cells in the homozygous humanized CD40 mice (FIG. 8F).

FIG. 9 shows PCR results for CD40 knockout mice. KO-1 and KO-11 were CD40 knockout mice. WT indicates wildtype.

FIG. 10. The average weight of the different groups of humanized CD40 heterozygous mice that were injected with mouse colon cancer cells MC38, and were treated with 6 different anti-human CD40 antibodies (3 mg/kg).

FIG. 11. The percentage change of average weight of the different groups of humanized CD40 heterozygous mice that were injected with mouse colon cancer cells MC38, and were treated with 6 different anti-human CD40 antibodies (3 mg/kg).

FIG. 12. The average tumor volume in different groups of humanized CD40 heterozygous mice that were injected with mouse colon cancer cells MC38, and were treated with 6 different anti-human CD40 antibodies (3 mg/kg).

FIG. 13. The average weight of the different groups of humanized CD40 homozygous mice that were injected with mouse colon cancer cells MC38, and were treated with 3 different anti-human CD40 antibodies (3 mg/kg).

FIG. 14. The percentage change of average weight of the different groups of humanized CD40 homozygous mice that were injected with mouse colon cancer cells MC38, and were treated with 3 different anti-human CD40 antibodies (3 mg/kg).

FIG. 15. The average tumor volume in different groups of humanized CD40 homozygous mice that were injected with mouse colon cancer cells MC38, and were treated with 3 different anti-human CD40 antibodies (3 mg/kg).

FIGS. 16A-16B show identification results from PCR. − indicates wildtype. + is the humanized CD40 heterozygous mouse positive control.

FIGS. 16C-16D show identification results from PCR. WT indicates wildtype, +/− is the humanized PD-1 heterozygous mouse positive control, −/− is the humanized PD-1 homozygous mouse positive control.

FIGS. 17A-17F are flow cytometry results of wildtype C57BL/6 mice (FIGS. 17A, 17B, 17D, and 17E) and double humanized homozygous CD40^(H/H)/PD-1^(H/H) mice (FIGS. 17C, 17F). Mouse CD3 antibody was used to activate spleen cells in FIGS. 17B, 17C, 17E and 17F. Flow cytometry was performed with antibody against mouse CD40 (mCD40 PE) and antibody against human CD40 (hCD40 APC).

FIGS. 18A-18F are flow cytometry results of wildtype C57BL/6 mice (FIGS. 18A, 18B, 18D, and 18E) and double humanized homozygous CD40^(H/H)/PD-1^(H/H) mice (FIGS. 18C, 18F). Mouse CD3 antibody was used to activate spleen cells in FIGS. 18B, 18C, 18E and 18F. Flow cytometry was performed with antibody against mouse PD-1 (mPD-1 PE) and antibody against human PD-1 (hPD-1 FITC).

FIGS. 19A-19B show PCR identification results. WT is wildtype; PC is the humanized CD40 heterozygous mouse positive control.

FIGS. 19C-19D show PCR identification results. WT is wildtype; PC is the humanized PD-L1 homozygous mouse positive control.

FIG. 20 shows the alignment between mouse CD40 amino acid sequence (NP_035741.2; SEQ ID NO: 21) and human CD40 amino acid sequence (NP_001241.1; SEQ ID NO: 23).

FIG. 21 is a schematic diagram showing gene targeting strategy based on embryonic stem cells.

DETAILED DESCRIPTION

This disclosure relates to transgenic non-human animal with human or chimeric (e.g., humanized) CD40, and methods of use thereof.

CD40 is a member of the TNF-receptor superfamily. It is a costimulatory protein found on antigen presenting cells and is required for their activation. This receptor has been found to be essential in mediating a broad variety of immune and inflammatory responses including T cell-dependent immunoglobulin class switching, memory B cell development, and germinal center formation. The binding of CD154 (CD40 ligand) on T cells to CD40 activates antigen presenting cells and induces a variety of downstream effects. CD154 is expressed primarily by activated T lymphocytes.

Like some other members of the TNF receptor family, CD40 signaling is mediated by adapter molecules rather than by inherent signal-transduction activity of the CD40 cytoplasmic tail. The TNFR-receptor associated factor adaptor proteins TRAF1, TRAF2, TRAF6 and possibly TRAF5 interact with CD40 and serve as mediators of the signal transduction.

CD40 is constitutively expressed by antigen presenting cells, including dendritic cells, B cells, and macrophages. It can also be expressed by endothelial cells, smooth muscle cells, fibroblasts and epithelial cells. Consistent with its widespread expression on normal cells, CD40 is also expressed on a wide range of tumor cells, including non-Hodgkin's and Hodgkin's lymphomas, myeloma and some carcinomas including nasopharynx, bladder, cervix, kidney and ovary.

In the macrophage, the primary signal for activation is IFN-γ from Th1 type CD4 T cells. The secondary signal is CD154 on the T cell which binds CD40 on the macrophage cell surface. As a result, the macrophage expresses more CD40 and TNF receptors on its surface which helps increase the level of activation of macrophages. The increase in activation can e.g., lead to the destruction of ingested microbe or tumor cells. The B cell can present antigens to helper T cells. If an activated T cell recognizes the peptide presented by the B cell, the CD154 on the T cell binds to the B cell's CD40 receptor, causing B cell activation. The T cell also produces IL-2, which directly influences B cells. As a result of this stimulation, the B cell can undergo division, antibody isotype switching, and differentiation to plasma cells. The end-result is a B cell that is able to mass-produce specific antibodies against an antigenic target. Thus, CD40 antibodies can be potentially used as cancer therapies.

Experimental animal models are an indispensable research tool for studying the effects of these antibodies (e.g., CD40 antibodies). Common experimental animals include mice, rats, guinea pigs, hamsters, rabbits, dogs, monkeys, pigs, fish and so on. However, there are many differences between human and animal genes and protein sequences, and many human proteins cannot bind to the animal's homologous proteins to produce biological activity, leading to that the results of many clinical trials do not match the results obtained from animal experiments. A large number of clinical studies are in urgent need of better animal models. With the continuous development and maturation of genetic engineering technologies, the use of human cells or genes to replace or substitute an animal's endogenous similar cells or genes to establish a biological system or disease model closer to human, and establish the humanized experimental animal models (humanized animal model) has provided an important tool for new clinical approaches or means. In this context, the genetically engineered animal model, that is, the use of genetic manipulation techniques, the use of human normal or mutant genes to replace animal homologous genes, can be used to establish the genetically modified animal models that are closer to human gene systems. The humanized animal models have various important applications. For example, due to the presence of human or humanized genes, the animals can express or express in part of the proteins with human functions, so as to greatly reduce the differences in clinical trials between humans and animals, and provide the possibility of drug screening at animal levels.

Unless otherwise specified, the practice of the methods described herein can take advantage of the techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA and immunology. These techniques are explained in detail in the following literature, for examples: Molecular Cloning A Laboratory Manual, 2nd Ed., ed. By Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1989); DNA Cloning, Volumes I and II (D. N. Glovered., 1985); Oligonucleotide Synthesis (M. J. Gaited., 1984); Mullis et al U.S. Pat. No. 4,683,195; Nucleic Acid Hybridization (B. D. Hames & S. J. Higginseds. 1984); Transcription And Translation (B. D. Hames & S. J. Higginseds. 1984); Culture Of Animal Cell (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984), the series, Methods In ENZYMOLOGY (J. Abelson and M. Simon, eds.-in-chief, Academic Press, Inc., New York), specifically, Vols. 154 and 155 (Wu et al. eds.) and Vol. 185, “Gene Expression Technology” (D. Goeddel, ed.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Caloseds., 1987, Cold Spring Harbor Laboratory); Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Hand book Of Experimental Immunology, Volumes V (D. M. Weir and C. C. Blackwell, eds., 1986); and Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986); each of which is incorporated herein by reference in its entirety.

CD40

CD40 (also known as Tumor Necrosis Factor Receptor Superfamily Member 5 or TNFRSF5) is a tumor necrosis factor receptor superfamily member expressed on antigen presenting cells (APC) such as dendritic cells (DC), macrophages, B cells, and monocytes as well as many non-immune cells and a wide range of tumors. Interaction with its trimeric ligand CD154 on activated T helper cells results in APC activation, leading to the induction of adaptive immunity.

Physiologically, signaling via CD40 on APC is thought to represent a major component of T cell help and mediates in large part the capacity of helper T cells to license APC. Ligation of CD40 on DC, for example, induces increased surface expression of costimulatory and MHC molecules, production of proinflammatory cytokines, and enhanced T cell triggering. CD40 ligation on resting B cells increases antigen-presenting function and proliferation.

In pre-clinical models, rat anti-mouse CD40 mAb show remarkable therapeutic activity in the treatment of CD40+ B-cell lymphomas (with 80-100% of mice cured and immune to re-challenge in a CD8 T-cell dependent manner) and are also effective in various CD40-negative tumors. These mAb are able to clear bulk tumors from mice with near terminal disease. To date, several CD40 mAb have been investigated in clinical trials: CP-870,893 (Pfizer and VLST), dacetuzumab (Seattle Genetics), Chi Lob 7/4 (University of Southampton), and lucatumumab (Novartis). They have been used for treating melanoma, pancreatic carcinoma, mesothelioma, hematological malignancies, especially Non-Hodgkin's lymphoma, lymphoma, chronic lymphocytic leukemia, and advanced solid tumors.

These therapeutic antibodies show diverse activities ranging from strong agonism (CP-870,893) to antagonism (lucatumumab). Currently there is no satisfactory explanation for this heterogeneity. The primary mechanistic rationale invoked for agonistic CD40 mAb is to activate host APC in order to induce clinically meaningful anti-tumor T-cell responses in patients. These include T cell-independent but macrophage-dependent triggering of tumor regression. CD40-activated macrophages can become tumoricidal, and least in pancreatic cancer, may also facilitate the depletion of tumor stroma which induces tumor collapse in vivo. Importantly, these mechanisms do not require expression of CD40 by the tumor, which has justified inclusion of patients with a broad range of tumors in many of the clinical trials. Insofar as these strategies aim to activate DC, macrophages, or both, the goal is not necessarily for the CD40 mAb to kill the cell it binds to, for example, via complement mediated cytotoxicity (CMC) or antibody dependent cellular cytoxicity (ADCC). Thus, by design, the strong agonistic antibody does not mediate CMC or ADCC.

In contrast, other human CD40 mAb can mediate CMC and ADCC against CD40+ tumors, such as nearly all B cell malignancies, a fraction of melanomas, and certain carcinomas. Finally, there is some evidence that ligation of CD40 on tumor cells promotes apoptosis and that this can be accomplished without engaging any immune effector pathway. This has been shown for CD40+ B cell malignancies and certain solid tumors such as CD40+ carcinomas and melanomas.

A detailed description of CD40 and its function can be found, e.g., in Vonderheide et al., “Agonistic CD40 antibodies and cancer therapy.” (2013): 1035-1043; Beatty, et al. “CD40 agonists alter tumor stroma and show efficacy against pancreatic carcinoma in mice and humans.” Science 331.6024 (2011): 1612-1616; Vonderheide, et al. “Clinical activity and immune modulation in cancer patients treated with CP-870,893, a novel CD40 agonist monoclonal antibody.” Journal of Clinical Oncology 25.7 (2007): 876-883; each of which is incorporated by reference in its entirety.

In human genomes, CD40 gene (Gene ID: 958) locus has nine exons, exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, and exon 9 (FIG. 3). The CD40 protein also has an extracellular region, a transmembrane region, and a cytoplasmic region, and the signal peptide is located at the extracellular region of CD40. The nucleotide sequence for human CD40 mRNA is NM_001250.5 (SEQ ID NO: 22), and the amino acid sequence for human CD40 is NP_001241.1 (SEQ ID NO: 23). The location for each exon and each region in human CD40 nucleotide sequence and amino acid sequence is listed below:

TABLE 1 NM_001250.5 NP_001241.1 Human CD40 1629 bp 277 aa (approximate location) (SEQ ID NO: 22) (SEQ ID NO: 23) Exon 1  1-141  1-17 Exon 2 142-220 18-43 Exon 3 221-346 44-85 Exon 4 347-493  86-134 Exon 5 494-587 135-166 Exon 6 588-649 167-186 Exon 7 650-736 187-215 Exon 8 737-765 216-225 Exon 9  766-1629 226-277 Signal peptide  91-150  1-20 Extracellular region 151-669  21-193 (excluding signal peptide region) Transmembrane region 670-735 194-215 Cytoplasmic region 736-921 216-277 Donor region in Example 148-666  20-192

In mice, CD40 gene locus has nine exons, exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, and exon 9 (FIG. 3). The mouse CD40 protein also has an extracellular region, a transmembrane region, and a cytoplasmic region, and the signal peptide is located at the extracellular region of CD40. The nucleotide sequence for mouse CD40 cDNA is NM_011611.2 (SEQ ID NO: 20), the amino acid sequence for mouse CD40 is NP_035741.2 (SEQ ID NO: 21). The location for each exon and each region in the mouse CD40 nucleotide sequence and amino acid sequence is listed below:

TABLE 2 NM_011611.2 NP_035741.2 Mouse CD40 1683 bp 289 aa (approximate location) (SEQ ID NO: 20) (SEQ ID NO: 21) Exon 1  1-123  1-17 Exon 2 124-202 18-43 Exon 3 203-328 44-85 Exon 4 329-475  86-134 Exon 5 476-569 135-166 Exon 6 570-631 167-186 Exon 7 632-718 187-215 Exon 8 719-750 216-226 Exon 9  751-1683 227-289 Signal peptide  73-129  1-19 Extracellular region 130-651  20-193 (excluding signal peptide region) Transmembrane region 652-717 194-215 Cytoplasmic region 718-939 216-289 Replaced region in Example 130-648  20-192

The mouse CD40 gene (Gene ID: 21939) is located in in Chromosome 2 of the mouse genome, which is located from 165055608-165071654 of NC_000068.7 (GRCm38.p4 (GCF_000001635.24)). The 5′-UTR is from 165055636 to 165055707, exon 1 is from 165055636 to 165055758, the first intron is from 165055759 to 165062285, exon 2 is from 165062286 to 165062364, the second intron is from 165062365 to 165062660, exon 3 is from 165062661 to 165062786, the third intron is from 165062787 to 165063021, exon 4 is from 165063022 to 165063168, the fourth intron is from 165063169 to 165063467, exon 5 is from 165063468 to 165063561, the fifth intron is from 165063562 to Ser. No. 16/506,502, exon 6 is from 165066503 to 165066564, the sixth intron is from 165066565 to 165069628, exon 7 is from 165069629 to 165069715, the seventh intron is from 165069716 to 165069816, exon 8 is from 165069,817 to 165069848, the eighth intron is from 165069849 to 165070721, exon 9 is from 165070722 to 165072948, the 3′-UTR is from 165070914 to 165072948, based on transcript NM_011611.2. All relevant information for mouse CD40 locus can be found in the NCBI website with Gene ID: 21939, which is incorporated by reference herein in its entirety.

FIG. 20 shows the alignment between mouse CD40 amino acid sequence (NP_035741.2; SEQ ID NO: 21) and human CD40 amino acid sequence (NP_001241.1; SEQ ID NO: 23). Thus, the corresponding amino acid residue or region between human and mouse CD40 can be found in FIG. 20.

CD40 genes, proteins, and locus of the other species are also known in the art. For example, the gene ID for CD40 in Rattus norvegicus is 171369, the gene ID for CD40 in Macaca mulatta (Rhesus monkey) is 707749, the gene ID for CD40 in Canis lupus familiaris (dog) is 403469, and the gene ID for CD40 in Cavia porcellus (domestic guinea pig) is 100728791. The relevant information for these genes (e.g., intron sequences, exon sequences, amino acid residues of these proteins) can be found, e.g., in NCBI database, which is incorporated by reference herein in its entirety.

The present disclosure provides human or chimeric (e.g., humanized) CD40 nucleotide sequence and/or amino acid sequences. In some embodiments, the entire sequence of mouse exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, exon 9, signal peptide, extracellular region, transmembrane region, and/or cytoplasmic region are replaced by the corresponding human sequence. In some embodiments, a “region” or “portion” of mouse exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, exon 9, signal peptide, extracellular region, transmembrane region, and/or cytoplasmic region are replaced by the corresponding human sequence. The term “region” or “portion” can refer to at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 250, 300, 350, 400, 500, or 600 nucleotides, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 amino acid residues. In some embodiments, the “region” or “portion” can be at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% identical to exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, exon 9, signal peptide, extracellular region, transmembrane region, or cytoplasmic region. In some embodiments, a region, a portion, or the entire sequence of mouse exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, and/or exon 9 (e.g., exon 2, exon 3, exon 4, exon 5, exon 6, exon 7) are replaced by the human exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, and/or exon 9 (e.g., exon 2, exon 3, exon 4, exon 5, exon 6, exon 7) sequence.

In some embodiments, the present disclosure also provides a chimeric (e.g., humanized) CD40 nucleotide sequence and/or amino acid sequences, wherein in some embodiments, at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% of the sequence are identical to or derived from mouse CD40 mRNA sequence (e.g., SEQ ID NO: 20), mouse CD40 amino acid sequence (e.g., SEQ ID NO: 21), or a portion thereof (e.g., exon 2, exon 3, exon 4, exon 5, exon 6, and exon 7); and in some embodiments, at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% of the sequence are identical to or derived from human CD40 mRNA sequence (e.g., SEQ ID NO: 22), human CD40 amino acid sequence (e.g., SEQ ID NO: 23), or a portion thereof (e.g., exon 2, exon 3, exon 4, exon 5, exon 6, and exon 7).

In some embodiments, the sequence encoding amino acids 20-192 of mouse CD40 (SEQ ID NO: 21) is replaced. In some embodiments, the sequence is replaced by a sequence encoding a corresponding region of human CD40 (e.g., amino acids 20-192 of human CD40 (SEQ ID NO: 23)).

In some embodiments, the nucleic acids as described herein are operably linked to a promotor or regulatory element, e.g., an endogenous mouse CD40 promotor, an inducible promoter, an enhancer, and/or mouse or human regulatory elements.

In some embodiments, the nucleic acid sequence has at least a portion (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 30, 40, 50, 60, 70, 80, 90, or 100 nucleotides, e.g., contiguous or non-contiguous nucleotides) that are different from a portion of or the entire mouse CD40 nucleotide sequence (e.g., exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, or NM_011611.2 (SEQ ID NO: 20)).

In some embodiments, the nucleic acid sequence has at least a portion (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 30, 40, 50, 60, 70, 80, 90, or 100 nucleotides, e.g., contiguous or non-contiguous nucleotides) that is the same as a portion of or the entire mouse CD40 nucleotide sequence (e.g., exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, or NM_011611.2 (SEQ ID NO: 20)).

In some embodiments, the nucleic acid sequence has at least a portion (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 30, 40, 50, 60, 70, 80, 90, or 100 nucleotides, e.g., contiguous or non-contiguous nucleotides) that is different from a portion of or the entire human CD40 nucleotide sequence (e.g., exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, or NM_001250.5 (SEQ ID NO: 22)).

In some embodiments, the nucleic acid sequence has at least a portion (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 30, 40, 50, 60, 70, 80, 90, or 100 nucleotides, e.g., contiguous or non-contiguous nucleotides) that is the same as a portion of or the entire human CD40 nucleotide sequence (e.g., exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, or NM_001250.5 (SEQ ID NO: 22)).

In some embodiments, the amino acid sequence has at least a portion (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 30, 40, 50, 60, 70, 80, 90, or 100 amino acid residues, e.g., contiguous or non-contiguous amino acid residues) that is different from a portion of or the entire mouse CD40 amino acid sequence (e.g., exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, or NP_035741.2 (SEQ ID NO: 21)).

In some embodiments, the amino acid sequence has at least a portion (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 30, 40, 50, 60, 70, 80, 90, or 100 amino acid residues, e.g., contiguous or non-contiguous amino acid residues) that is the same as a portion of or the entire mouse CD40 amino acid sequence (e.g., exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, or NP_035741.2 (SEQ ID NO: 21)).

In some embodiments, the amino acid sequence has at least a portion (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 30, 40, 50, 60, 70, 80, 90, or 100 amino acid residues, e.g., contiguous or non-contiguous amino acid residues) that is different from a portion of or the entire human CD40 amino acid sequence (e.g., exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, or NP_001241.1 (SEQ ID NO: 23)).

In some embodiments, the amino acid sequence has at least a portion (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 30, 40, 50, 60, 70, 80, 90, or 100 amino acid residues, e.g., contiguous or non-contiguous amino acid residues) that is the same as a portion of or the entire human CD40 amino acid sequence (e.g., exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, or NP_001241.1 (SEQ ID NO: 23)).

The present disclosure also provides a humanized CD40 mouse amino acid sequence, wherein the amino acid sequence is selected from the group consisting of:

a) an amino acid sequence shown in SEQ ID NO: 27;

b) an amino acid sequence having a homology of at least 90% with or at least 90% identical to the amino acid sequence shown in SEQ ID NO: 27;

c) an amino acid sequence encoded by a nucleic acid sequence, wherein the nucleic acid sequence is able to hybridize to a nucleotide sequence encoding the amino acid shown in SEQ ID NO: 27 under a low stringency condition or a strict stringency condition;

d) an amino acid sequence having a homology of at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, or at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequence shown in SEQ ID NO: 27;

e) an amino acid sequence that is different from the amino acid sequence shown in SEQ ID NO: 27 by no more than 10, 9, 8, 7, 6, 5, 4, 3, 2 or no more than 1 amino acid; or

f) an amino acid sequence that comprises a substitution, a deletion and/or insertion of one or more amino acids to the amino acid sequence shown in SEQ ID NO: 27.

The present disclosure also relates to a CD40 nucleic acid (e.g., DNA or RNA) sequence, wherein the nucleic acid sequence can be selected from the group consisting of:

a) a nucleic acid sequence as shown in SEQ ID NO: 25, or a nucleic acid sequence encoding a homologous CD40 amino acid sequence of a humanized mouse;

b) a nucleic acid sequence that is shown in SEQ ID NO: 26;

c) a nucleic acid sequence that is able to hybridize to the nucleotide sequence as shown in SEQ ID NO: 25 or SEQ ID NO: 26 under a low stringency condition or a strict stringency condition;

d) a nucleic acid sequence that has a homology of at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, or at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the nucleotide sequence as shown in SEQ ID NO: 25 or SEQ ID NO: 26;

e) a nucleic acid sequence that encodes an amino acid sequence, wherein the amino acid sequence has a homology of at least 90% with or at least 90% identical to the amino acid sequence shown in SEQ ID NO: 27;

f) a nucleic acid sequence that encodes an amino acid sequence, wherein the amino acid sequence has a homology of at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% with, or at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequence shown in SEQ ID NO: 27;

g) a nucleic acid sequence that encodes an amino acid sequence, wherein the amino acid sequence is different from the amino acid sequence shown in SEQ ID NO: 27 by no more than 10, 9, 8, 7, 6, 5, 4, 3, 2 or no more than 1 amino acid; and/or

h) a nucleic acid sequence that encodes an amino acid sequence, wherein the amino acid sequence comprises a substitution, a deletion and/or insertion of one or more amino acids to the amino acid sequence shown in SEQ ID NO: 27.

The present disclosure further relates to a CD40 genomic DNA sequence of a humanized mouse. The DNA sequence is obtained by a reverse transcription of the mRNA obtained by transcription thereof is consistent with or complementary to the DNA sequence homologous to the sequence shown in SEQ ID NO: 25 or SEQ ID NO: 26.

The disclosure also provides an amino acid sequence that has a homology of at least 90% with, or at least 90% identical to the sequence shown in SEQ ID NO: 27, and has protein activity. In some embodiments, the homology with the sequence shown in SEQ ID NO: 27 is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99%. In some embodiments, the foregoing homology is at least about 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 80%, or 85%.

In some embodiments, the percentage identity with the sequence shown in SEQ ID NO: 27 is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99%. In some embodiments, the foregoing percentage identity is at least about 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 80%, or 85%.

The disclosure also provides a nucleotide sequence that has a homology of at least 90%, or at least 90% identical to the sequence shown in SEQ ID NO: 25 or SEQ ID NO: 26, and encodes a polypeptide that has protein activity. In some embodiments, the homology with the sequence shown in SEQ ID NO: 25 or SEQ ID NO: 26 is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99%. In some embodiments, the foregoing homology is at least about 50%, 55%, 60%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 80%, or 85%.

In some embodiments, the percentage identity with the sequence shown in SEQ ID NO: 25 or SEQ ID NO: 26 is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99%. In some embodiments, the foregoing percentage identity is at least about 50%, 55%, 60%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 80%, or 85%.

The disclosure also provides a nucleic acid sequence that is at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to any nucleotide sequence as described herein, and an amino acid sequence that is at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical to any amino acid sequence as described herein. In some embodiments, the disclosure relates to nucleotide sequences encoding any peptides that are described herein, or any amino acid sequences that are encoded by any nucleotide sequences as described herein. In some embodiments, the nucleic acid sequence is less than 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 150, 200, 250, 300, 350, 400, 500, or 600 nucleotides. In some embodiments, the amino acid sequence is less than 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or 200 amino acid residues.

In some embodiments, the amino acid sequence (i) comprises an amino acid sequence; or (ii) consists of an amino acid sequence, wherein the amino acid sequence is any one of the sequences as described herein.

In some embodiments, the nucleic acid sequence (i) comprises a nucleic acid sequence; or (ii) consists of a nucleic acid sequence, wherein the nucleic acid sequence is any one of the sequences as described herein.

To determine the percent identity of two amino acid sequences, or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). The length of a reference sequence aligned for comparison purposes is at least 80% of the length of the reference sequence, and in some embodiments is at least 90%, 95%, or 100%. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences. For purposes of the present disclosure, the comparison of sequences and determination of percent identity between two sequences can be accomplished using a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.

The percentage of residues conserved with similar physicochemical properties (percent homology), e.g. leucine and isoleucine, can also be used to measure sequence similarity. Families of amino acid residues having similar physicochemical properties have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). The homology percentage, in many cases, is higher than the identity percentage.

Cells, tissues, and animals (e.g., mouse) are also provided that comprise the nucleotide sequences as described herein, as well as cells, tissues, and animals (e.g., mouse) that express human or chimeric (e.g., humanized) CD40 from an endogenous non-human CD40 locus.

Genetically Modified Animals

As used herein, the term “genetically-modified non-human animal” refers to a non-human animal having exogenous DNA in at least one chromosome of the animal's genome. In some embodiments, at least one or more cells, e.g., at least 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50% of cells of the genetically-modified non-human animal have the exogenous DNA in its genome. The cell having exogenous DNA can be various kinds of cells, e.g., an endogenous cell, a somatic cell, an immune cell, a T cell, a B cell, an antigen presenting cell, a macrophage, a dendritic cell, a germ cell, a blastocyst, or an endogenous tumor cell. In some embodiments, genetically-modified non-human animals are provided that comprise a modified endogenous CD40 locus that comprises an exogenous sequence (e.g., a human sequence), e.g., a replacement of one or more non-human sequences with one or more human sequences. The animals are generally able to pass the modification to progeny, i.e., through germline transmission.

As used herein, the term “chimeric gene” or “chimeric nucleic acid” refers to a gene or a nucleic acid, wherein two or more portions of the gene or the nucleic acid are from different species, or at least one of the sequences of the gene or the nucleic acid does not correspond to the wildtype nucleic acid in the animal. In some embodiments, the chimeric gene or chimeric nucleic acid has at least one portion of the sequence that is derived from two or more different sources, e.g., sequences encoding different proteins or sequences encoding the same (or homologous) protein of two or more different species. In some embodiments, the chimeric gene or the chimeric nucleic acid is a humanized gene or humanized nucleic acid.

As used herein, the term “chimeric protein” or “chimeric polypeptide” refers to a protein or a polypeptide, wherein two or more portions of the protein or the polypeptide are from different species, or at least one of the sequences of the protein or the polypeptide does not correspond to wildtype amino acid sequence in the animal. In some embodiments, the chimeric protein or the chimeric polypeptide has at least one portion of the sequence that is derived from two or more different sources, e.g., same (or homologous) proteins of different species. In some embodiments, the chimeric protein or the chimeric polypeptide is a humanized protein or a humanized polypeptide.

In some embodiments, the chimeric gene or the chimeric nucleic acid is a humanized CD40 gene or a humanized CD40 nucleic acid. In some embodiments, at least one or more portions of the gene or the nucleic acid is from the human CD40 gene, at least one or more portions of the gene or the nucleic acid is from a non-human CD40 gene. In some embodiments, the gene or the nucleic acid comprises a sequence that encodes a CD40 protein. The encoded CD40 protein is functional or has at least one activity of the human CD40 protein or the non-human CD40 protein, e.g., binding with human or non-human CD40L (CD154), increasing the level of activation of macrophages, activating B cell (e.g., inducing B cell division, antibody isotype switching, differentiation to plasma cells, production of antibodies), inducing expression of costimulatory and MHC molecules on dendritic cells, increasing production of proinflammatory cytokines, increasing antigen-presenting function, inducing activation and proliferation of immune cells (e.g., B cells, macrophages, dendritic cells), increasing the production of cytokines, and/or upregulating the immune response.

In some embodiments, the chimeric protein or the chimeric polypeptide is a humanized CD40 protein or a humanized CD40 polypeptide. In some embodiments, at least one or more portions of the amino acid sequence of the protein or the polypeptide is from a human CD40 protein, and at least one or more portions of the amino acid sequence of the protein or the polypeptide is from a non-human CD40 protein. The humanized CD40 protein or the humanized CD40 polypeptide is functional or has at least one activity of the human CD40 protein or the non-human CD40 protein.

The genetically modified non-human animal can be various animals, e.g., a mouse, rat, rabbit, pig, bovine (e.g., cow, bull, buffalo), deer, sheep, goat, chicken, cat, dog, ferret, primate (e.g., marmoset, rhesus monkey). For the non-human animals where suitable genetically modifiable embryonic stem (ES) cells are not readily available, other methods are employed to make a non-human animal comprising the genetic modification. Such methods include, e.g., modifying a non-ES cell genome (e.g., a fibroblast or an induced pluripotent cell) and employing nuclear transfer to transfer the modified genome to a suitable cell, e.g., an oocyte, and gestating the modified cell (e.g., the modified oocyte) in a non-human animal under suitable conditions to form an embryo. These methods are known in the art, and are described, e.g., in A. Nagy, et al., “Manipulating the Mouse Embryo: A Laboratory Manual (Third Edition),” Cold Spring Harbor Laboratory Press, 2003, which is incorporated by reference herein in its entirety.

In one aspect, the animal is a mammal, e.g., of the superfamily Dipodoidea or Muroidea. In some embodiments, the genetically modified animal is a rodent. The rodent can be selected from a mouse, a rat, and a hamster. In some embodiments, the genetically modified animal is from a family selected from Calomyscidae (e.g., mouse-like hamsters), Cricetidae (e.g., hamster, New World rats and mice, voles), Muridae (true mice and rats, gerbils, spiny mice, crested rats), Nesomyidae (climbing mice, rock mice, with-tailed rats, Malagasy rats and mice), Platacanthomyidae (e.g., spiny dormice), and Spalacidae (e.g., mole rates, bamboo rats, and zokors). In some embodiments, the genetically modified rodent is selected from a true mouse or rat (family Muridae), a gerbil, a spiny mouse, and a crested rat. In some embodiments, the non-human animal is a mouse.

In some embodiments, the animal is a mouse of a C57BL strain selected from C57BL/A, C57BL/An, C57BL/GrFa, C57BL/KaLwN, C57BL/6, C57BL/6J, C57BL/6ByJ, C57BL/6NJ, C57BL/10, C57BL/10ScSn, C57BL/10Cr, and C57BL/01a. In some embodiments, the mouse is a 129 strain selected from the group consisting of a strain that is 129P1, 129P2, 129P3, 129X1, 129S1 (e.g., 12951/SV, 12951/SvIm), 129S2, 129S4, 129S5, 12959/SvEvH, 129S6 (129/SvEvTac), 129S7, 129S8, 129T1, 129T2. These mice are described, e.g., in Festing et al., Revised nomenclature for strain 129 mice, Mammalian Genome 10: 836 (1999); Auerbach et al., Establishment and Chimera Analysis of 129/SvEv- and C57BL/6-Derived Mouse Embryonic Stem Cell Lines (2000), both of which are incorporated herein by reference in the entirety. In some embodiments, the genetically modified mouse is a mix of the 129 strain and the C57BL/6 strain. In some embodiments, the mouse is a mix of the 129 strains, or a mix of the BL/6 strains. In some embodiments, the mouse is a BALB strain, e.g., BALB/c strain. In some embodiments, the mouse is a mix of a BALB strain and another strain. In some embodiments, the mouse is from a hybrid line (e.g., 50% BALB/c-50% 12954/Sv; or 50% C57BL/6-50% 129).

In some embodiments, the animal is a rat. The rat can be selected from a Wistar rat, an LEA strain, a Sprague Dawley strain, a Fischer strain, F344, F6, and Dark Agouti. In some embodiments, the rat strain is a mix of two or more strains selected from the group consisting of Wistar, LEA, Sprague Dawley, Fischer, F344, F6, and Dark Agouti.

The animal can have one or more other genetic modifications, and/or other modifications, that are suitable for the particular purpose for which the humanized CD40 animal is made. For example, suitable mice for maintaining a xenograft (e.g., a human cancer or tumor), can have one or more modifications that compromise, inactivate, or destroy the immune system of the non-human animal in whole or in part. Compromise, inactivation, or destruction of the immune system of the non-human animal can include, for example, destruction of hematopoietic cells and/or immune cells by chemical means (e.g., administering a toxin), physical means (e.g., irradiating the animal), and/or genetic modification (e.g., knocking out one or more genes). Non-limiting examples of such mice include, e.g., NOD mice, SCID mice, NOD/SCID mice, IL2Rγ knockout mice, NOD/SCID/γcnull mice (Ito, M. et al., NOD/SCID/γcnull mouse: an excellent recipient mouse model for engraftment of human cells, Blood 100(9): 3175-3182, 2002), nude mice, and Rag1 and/or Rag2 knockout mice. These mice can optionally be irradiated, or otherwise treated to destroy one or more immune cell type. Thus, in various embodiments, a genetically modified mouse is provided that can include a humanization of at least a portion of an endogenous non-human CD40 locus, and further comprises a modification that compromises, inactivates, or destroys the immune system (or one or more cell types of the immune system) of the non-human animal in whole or in part. In some embodiments, modification is, e.g., selected from the group consisting of a modification that results in NOD mice, SCID mice, NOD/SCID mice, IL-2Rγ knockout mice, NOD/SCID/γc null mice, nude mice, Rag1 and/or Rag2 knockout mice, and a combination thereof. These genetically modified animals are described, e.g., in US20150106961, which is incorporated herein by reference in its entirety. In some embodiments, the mouse can include a replacement of all or part of mature CD40 coding sequence with human mature CD40 coding sequence.

Genetically modified non-human animals that comprise a modification of an endogenous non-human CD40 locus. In some embodiments, the modification can comprise a human nucleic acid sequence encoding at least a portion of a mature CD40 protein (e.g., at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, or 99% identical to the mature CD40 protein sequence). Although genetically modified cells are also provided that can comprise the modifications described herein (e.g., ES cells, somatic cells), in many embodiments, the genetically modified non-human animals comprise the modification of the endogenous CD40 locus in the germline of the animal.

Genetically modified animals can express a human CD40 and/or a chimeric (e.g., humanized) CD40 from endogenous mouse loci, wherein the endogenous mouse CD40 gene has been replaced with a human CD40 gene and/or a nucleotide sequence that encodes a region of human CD40 sequence or an amino acid sequence that is at least 10%, 20%, 30%, 40%, 50%, 60%, 70&, 80%, 90%, 95%, 96%, 97%, 98%, or 99% identical to the human CD40 sequence. In various embodiments, an endogenous non-human CD40 locus is modified in whole or in part to comprise human nucleic acid sequence encoding at least one protein-coding sequence of a mature CD40 protein.

In some embodiments, the genetically modified mice express the human CD40 and/or chimeric CD40 (e.g., humanized CD40) from endogenous loci that are under control of mouse promoters and/or mouse regulatory elements. The replacement(s) at the endogenous mouse loci provide non-human animals that express human CD40 or chimeric CD40 (e.g., humanized CD40) in appropriate cell types and in a manner that does not result in the potential pathologies observed in some other transgenic mice known in the art. The human CD40 or the chimeric CD40 (e.g., humanized CD40) expressed in animal can maintain one or more functions of the wildtype mouse or human CD40 in the animal. For example, human or non-human CD40 ligands (e.g., CD154) can bind to the expressed CD40, upregulate immune response, e.g., upregulate immune response by at least 10%, 20%, 30%, 40%, or 50%. Furthermore, in some embodiments, the animal does not express endogenous CD40. As used herein, the term “endogenous CD40” refers to CD40 protein that is expressed from an endogenous CD40 nucleotide sequence of the non-human animal (e.g., mouse) before any genetic modification.

The genome of the animal can comprise a sequence encoding an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% identical to human CD40 (NP_001241.1) (SEQ ID NO: 23). In some embodiments, the genome comprises a sequence encoding an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% identical to SEQ ID NO: 27.

The genome of the genetically modified animal can comprise a replacement at an endogenous CD40 gene locus of a sequence encoding a region of endogenous CD40 with a sequence encoding a corresponding region of human CD40. In some embodiments, the sequence that is replaced is any sequence within the endogenous CD40 gene locus, e.g., exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, exon 9, 5′-UTR, 3′-UTR, the first intron, the second intron, and the third intron, the fourth intron, the fifth intron, the sixth intron, the seventh intron, the eighth intron etc. In some embodiments, the sequence that is replaced is within the regulatory region of the endogenous CD40 gene. In some embodiments, the sequence that is replaced is exon 2, exon 3, exon 4, exon 5, exon 6, exon 7 or part thereof, of an endogenous mouse CD40 gene locus.

The genetically modified animal can have one or more cells expressing a human or chimeric CD40 (e.g., humanized CD40) having an extracellular region and a cytoplasmic region, wherein the extracellular region comprises a sequence that is at least 50%, 60%, 70%, 80%, 90%, 95%, 99% identical to the extracellular region of human CD40. In some embodiments, the extracellular region of the humanized CD40 has a sequence that has at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, or 180 amino acids (e.g., contiguously or non-contiguously) that are identical to human CD40. Because human CD40 and non-human CD40 (e.g., mouse CD40) sequences, in many cases, are different, antibodies that bind to human CD40 will not necessarily have the same binding affinity with non-human CD40 or have the same effects to non-human CD40. Therefore, the genetically modified animal having a human or a humanized extracellular region can be used to better evaluate the effects of anti-human CD40 antibodies in an animal model. In some embodiments, the genome of the genetically modified animal comprises a sequence encoding an amino acid sequence that corresponds to part or the entire sequence of exon 2, exon 3, exon 4, exon 5, exon 6, and/or exon 7 of human CD40, part or the entire sequence of extracellular region of human CD40 (with or without signal peptide), or part or the entire sequence of amino acids 20-192 of SEQ ID NO: 23.

In some embodiments, the non-human animal can have, at an endogenous CD40 gene locus, a nucleotide sequence encoding a chimeric human/non-human CD40 polypeptide, wherein a human portion of the chimeric human/non-human CD40 polypeptide comprises a portion of human CD40 extracellular domain, and wherein the animal expresses a functional CD40 on a surface of a cell of the animal. The human portion of the chimeric human/non-human CD40 polypeptide can comprise a portion of exon 2, exon 3, exon 4, exon 5, exon 6, and/or exon 7 of human CD40. In some embodiments, the human portion of the chimeric human/non-human CD40 polypeptide can comprise a sequence that is at least 80%, 85%, 90%, 95%, or 99% identical to amino acids 20-192 of SEQ ID NO: 23.

In some embodiments, the non-human portion of the chimeric human/non-human CD40 polypeptide comprises transmembrane and/or cytoplasmic regions of an endogenous non-human CD40 polypeptide. There may be several advantages that are associated with the transmembrane and/or cytoplasmic regions of an endogenous non-human CD40 polypeptide. For example, once a CD40 ligand (e.g., CD154) or an anti-CD40 antibody binds to CD40, they can properly transmit extracellular signals into the cells and initiate the downstream pathway. A human or humanized transmembrane and/or cytoplasmic regions may not function properly in non-human animal cells. In some embodiments, a few extracellular amino acids that are close to the transmembrane region of CD40 are also derived from endogenous sequence. These amino acids can also be important for transmembrane signal transmission.

Furthermore, the genetically modified animal can be heterozygous with respect to the replacement at the endogenous CD40 locus, or homozygous with respect to the replacement at the endogenous CD40 locus.

In some embodiments, the humanized CD40 locus lacks a human CD40 5′-UTR. In some embodiment, the humanized CD40 locus comprises a rodent (e.g., mouse) 5′-UTR. In some embodiments, the humanization comprises a human 3′-UTR. In appropriate cases, it may be reasonable to presume that the mouse and human CD40 genes appear to be similarly regulated based on the similarity of their 5′-flanking sequence. As shown in the present disclosure, humanized CD40 mice that comprise a replacement at an endogenous mouse CD40 locus, which retain mouse regulatory elements but comprise a humanization of CD40 encoding sequence, do not exhibit pathologies. Both genetically modified mice that are heterozygous or homozygous for humanized CD40 are grossly normal.

The present disclosure further relates to a non-human mammal generated through the method mentioned above. In some embodiments, the genome thereof contains human gene(s).

In some embodiments, the non-human mammal is a rodent, and preferably, the non-human mammal is a mouse.

In some embodiments, the non-human mammal expresses a protein encoded by a humanized CD40 gene.

In addition, the present disclosure also relates to a tumor bearing non-human mammal model, characterized in that the non-human mammal model is obtained through the methods as described herein. In some embodiments, the non-human mammal is a rodent (e.g., a mouse).

The present disclosure further relates to a cell or cell line, or a primary cell culture thereof derived from the non-human mammal or an offspring thereof, or the tumor bearing non-human mammal; the tissue, organ or a culture thereof derived from the non-human mammal or an offspring thereof, or the tumor bearing non-human mammal; and the tumor tissue derived from the non-human mammal or an offspring thereof when it bears a tumor, or the tumor bearing non-human mammal.

The present disclosure also provides non-human mammals produced by any of the methods described herein. In some embodiments, a non-human mammal is provided; and the genetically modified animal contains the DNA encoding human or humanized CD40 in the genome of the animal.

In some embodiments, the non-human mammal comprises the genetic construct as described herein (e.g., gene construct as shown in FIG. 2 or FIG. 3). In some embodiments, a non-human mammal expressing human or humanized CD40 is provided. In some embodiments, the tissue-specific expression of human or humanized CD40 protein is provided.

In some embodiments, the expression of human or humanized CD40 in a genetically modified animal is controllable, as by the addition of a specific inducer or repressor substance.

Non-human mammals can be any non-human animal known in the art and which can be used in the methods as described herein. Preferred non-human mammals are mammals, (e.g., rodents). In some embodiments, the non-human mammal is a mouse.

Genetic, molecular and behavioral analyses for the non-human mammals described above can performed. The present disclosure also relates to the progeny produced by the non-human mammal provided by the present disclosure mated with the same or other genotypes.

The present disclosure also provides a cell line or primary cell culture derived from the non-human mammal or a progeny thereof. A model based on cell culture can be prepared, for example, by the following methods. Cell cultures can be obtained by way of isolation from a non-human mammal, alternatively cell can be obtained from the cell culture established using the same constructs and the standard cell transfection techniques. The integration of genetic constructs containing DNA sequences encoding human CD40 protein can be detected by a variety of methods.

There are many analytical methods that can be used to detect exogenous DNA, including methods at the level of nucleic acid (including the mRNA quantification approaches using reverse transcriptase polymerase chain reaction (RT-PCR) or Southern blotting, and in situ hybridization) and methods at the protein level (including histochemistry, immunoblot analysis and in vitro binding studies). In addition, the expression level of the gene of interest can be quantified by ELISA techniques well known to those skilled in the art. Many standard analysis methods can be used to complete quantitative measurements. For example, transcription levels can be measured using RT-PCR and hybridization methods including RNase protection, Southern blot analysis, RNA dot analysis (RNAdot) analysis. Immunohistochemical staining, flow cytometry, Western blot analysis can also be used to assess the presence of human or humanized CD40 protein.

Vectors

The present disclosure relates to a targeting vector, comprising: a) a DNA fragment homologous to the 5′ end of a region to be altered (5′ arm), which is selected from the CD40 gene genomic DNAs in the length of 100 to 10,000 nucleotides; b) a desired/donor DNA sequence encoding a donor region; and c) a second DNA fragment homologous to the 3′ end of the region to be altered (3′ arm), which is selected from the CD40 gene genomic DNAs in the length of 100 to 10,000 nucleotides.

In some embodiments, a) the DNA fragment homologous to the 5′ end of a conversion region to be altered (5′ arm) is selected from the nucleotide sequences that have at least 90% homology to the NCBI accession number NC_000068.7; c) the DNA fragment homologous to the 3′ end of the region to be altered (3′ arm) is selected from the nucleotide sequences that have at least 90% homology to the NCBI accession number NC_000068.7.

In some embodiments, a) the DNA fragment homologous to the 5′ end of a region to be altered (5′ arm) is selected from the nucleotides from the position 165060750 to the position 165062291 of the NCBI accession number NC_000068.7; c) the DNA fragment homologous to the 3′ end of the region to be altered (3′ arm) is selected from the nucleotides from the position 165069646 to the position 165071120 of the NCBI accession number NC_000068.7.

In some embodiments, the length of the selected genomic nucleotide sequence in the targeting vector can be more than about 3 kb, about 3.5 kb, about 4 kb, about 4.5 kb, about 5 kb, about 5.5 kb, or about 6 kb.

In some embodiments, the region to be altered is exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon8, and/or exon 9 of CD40 gene (e.g., exon 2, exon 3, exon 4, exon 5, exon 6, and/or exon 7 of mouse CD40 gene).

The targeting vector can further include a selected gene marker.

In some embodiments, the sequence of the 5′ arm is shown in SEQ ID NO: 28; and the sequence of the 3′ arm is shown in SEQ ID NO: 29.

In some embodiments, the sequence is derived from human (e.g., 46121826-46128154 of NC_000020.11). For example, the target region in the targeting vector is a part or entirety of the nucleotide sequence of a human CD40, preferably exon 2, exon 3, exon 4, exon 5, exon 6, and/or exon 7 of the human CD40. In some embodiments, the nucleotide sequence of the humanized CD40 encodes the entire or the part of human CD40 protein with the NCBI accession number NP_001241.1 (SEQ ID NO: 23).

The disclosure also relates to a cell comprising the targeting vectors as described above.

In addition, the present disclosure further relates to a non-human mammalian cell, having any one of the foregoing targeting vectors, and one or more in vitro transcripts of the construct as described herein. In some embodiments, the cell includes Cas9 mRNA or an in vitro transcript thereof.

In some embodiments, the genes in the cell are heterozygous. In some embodiments, the genes in the cell are homozygous.

In some embodiments, the non-human mammalian cell is a mouse cell. In some embodiments, the cell is a fertilized egg cell.

Methods of Making Genetically Modified Animals

Genetically modified animals can be made by several techniques that are known in the art, including, e.g., nonhomologous end-joining (NHEJ), homologous recombination (HR), zinc finger nucleases (ZFNs), transcription activator-like effector-based nucleases (TALEN), and the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system. In some embodiments, homologous recombination is used. In some embodiments, CRISPR-Cas9 genome editing is used to generate genetically modified animals. Many of these genome editing techniques are known in the art, and is described, e.g., in Yin et al., “Delivery technologies for genome editing,” Nature Reviews Drug Discovery 16.6 (2017): 387-399, which is incorporated by reference in its entirety. Many other methods are also provided and can be used in genome editing, e.g., micro-injecting a genetically modified nucleus into an enucleated oocyte, and fusing an enucleated oocyte with another genetically modified cell.

Thus, in some embodiments, the disclosure provides replacing in at least one cell of the animal, at an endogenous CD40 gene locus, a sequence encoding a region of an endogenous CD40 with a sequence encoding a corresponding region of human or chimeric CD40. In some embodiments, the replacement occurs in a germ cell, a somatic cell, a blastocyst, or a fibroblast, etc. The nucleus of a somatic cell or the fibroblast can be inserted into an enucleated oocyte.

FIG. 3 shows a humanization strategy for a mouse CD40 locus. In FIG. 3, the targeting strategy involves a vector comprising the 5′ end homologous arm, human CD40 gene fragment, 3′ homologous arm. The process can involve replacing endogenous CD40 sequence with human sequence by homologous recombination. In some embodiments, the cleavage at the upstream and the downstream of the target site (e.g., by zinc finger nucleases, TALEN or CRISPR) can result in DNA double strands break, and the homologous recombination is used to replace endogenous CD40 sequence with human CD40 sequence.

Thus, in some embodiments, the methods for making a genetically modified, humanized animal, can include the step of replacing at an endogenous CD40 locus (or site), a nucleic acid encoding a sequence encoding a region of endogenous CD40 with a sequence encoding a corresponding region of human CD40. The sequence can include a region (e.g., a part or the entire region) of exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, and/or exon 9 of a human CD40 gene. In some embodiments, the sequence includes a region of exon 2, exon 3, exon 4, exon 5, exon 6, and exon 7 of a human CD40 gene (e.g., amino acids 20-192 of SEQ ID NO: 23). In some embodiments, the region is located within the extracellular region of CD40. In some embodiments, the endogenous CD40 locus is exon 2, exon 3, exon 4, exon 5, exon 6, and/or exon 7 of mouse CD40.

In some embodiments, the methods of modifying a CD40 locus of a mouse to express a chimeric human/mouse CD40 peptide can include the steps of replacing at the endogenous mouse CD40 locus a nucleotide sequence encoding a mouse CD40 with a nucleotide sequence encoding a human CD40, thereby generating a sequence encoding a chimeric human/mouse CD40.

In some embodiments, the nucleotide sequence encoding the chimeric human/mouse CD40 can include a first nucleotide sequence encoding an extracellular region of mouse CD40 (with or without the mouse or human signal peptide sequence); a second nucleotide sequence encoding an extracellular region of human CD40; a third nucleotide sequence encoding a transmembrane and a cytoplasmic region of a mouse CD40.

In some embodiments, the nucleotide sequences as described herein do not overlap with each other (e.g., the first nucleotide sequence, the second nucleotide sequence, and/or the third nucleotide sequence do not overlap). In some embodiments, the amino acid sequences as described herein do not overlap with each other.

The present disclosure further provides a method for establishing a CD40 gene humanized animal model, involving the following steps:

(a) providing the cell (e.g. a fertilized egg cell) based on the methods described herein;

(b) culturing the cell in a liquid culture medium;

(c) transplanting the cultured cell to the fallopian tube or uterus of the recipient female non-human mammal, allowing the cell to develop in the uterus of the female non-human mammal;

(d) identifying the germline transmission in the offspring genetically modified humanized non-human mammal of the pregnant female in step (c).

In some embodiments, the non-human mammal in the foregoing method is a mouse (e.g., a C57BL/6 mouse).

In some embodiments, the non-human mammal in step (c) is a female with pseudo pregnancy (or false pregnancy).

In some embodiments, the fertilized eggs for the methods described above are C57BL/6 fertilized eggs. Other fertilized eggs that can also be used in the methods as described herein include, but are not limited to, FVB/N fertilized eggs, BALB/c fertilized eggs, DBA/1 fertilized eggs and DBA/2 fertilized eggs.

Fertilized eggs can come from any non-human animal, e.g., any non-human animal as described herein. In some embodiments, the fertilized egg cells are derived from rodents. The genetic construct can be introduced into a fertilized egg by microinjection of DNA. For example, by way of culturing a fertilized egg after microinjection, a cultured fertilized egg can be transferred to a false pregnant non-human animal, which then gives birth of a non-human mammal, so as to generate the non-human mammal mentioned in the methods described above.

Methods of Using Genetically Modified Animals

Replacement of non-human genes in a non-human animal with homologous or orthologous human genes or human sequences, at the endogenous non-human locus and under control of endogenous promoters and/or regulatory elements, can result in a non-human animal with qualities and characteristics that may be substantially different from a typical knockout-plus-transgene animal. In the typical knockout-plus-transgene animal, an endogenous locus is removed or damaged and a fully human transgene is inserted into the animal's genome and presumably integrates at random into the genome. Typically, the location of the integrated transgene is unknown; expression of the human protein is measured by transcription of the human gene and/or protein assay and/or functional assay. Inclusion in the human transgene of upstream and/or downstream human sequences are apparently presumed to be sufficient to provide suitable support for expression and/or regulation of the transgene.

In some cases, the transgene with human regulatory elements expresses in a manner that is unphysiological or otherwise unsatisfactory, and can be actually detrimental to the animal. The disclosure demonstrates that a replacement with human sequence at an endogenous locus under control of endogenous regulatory elements provides a physiologically appropriate expression pattern and level that results in a useful humanized animal whose physiology with respect to the replaced gene are meaningful and appropriate in the context of the humanized animal's physiology.

Genetically modified animals that express human or humanized CD40 protein, e.g., in a physiologically appropriate manner, provide a variety of uses that include, but are not limited to, developing therapeutics for human diseases and disorders, and assessing the toxicity and/or the efficacy of these human therapeutics in the animal models.

In various aspects, genetically modified animals are provided that express human or humanized CD40, which are useful for testing agents that can decrease or block the interaction between CD40 and CD40 ligands (e.g., CD154) or the interaction between CD40 and anti-human CD40 antibodies, testing whether an agent can increase or decrease the immune response, and/or determining whether an agent is an CD40 agonist or antagonist. The genetically modified animals can be, e.g., an animal model of a human disease, e.g., the disease is induced genetically (a knock-in or knockout). In various embodiments, the genetically modified non-human animals further comprise an impaired immune system, e.g., a non-human animal genetically modified to sustain or maintain a human xenograft, e.g., a human solid tumor or a blood cell tumor (e.g., a lymphocyte tumor, e.g., a B or T cell tumor).

In some embodiments, the genetically modified animals can be used for determining effectiveness of an anti-CD40 antibody for the treatment of cancer. The methods involve administering the anti-CD40 antibody (e.g., anti-human CD40 antibody) to the animal as described herein, wherein the animal has a tumor; and determining the inhibitory effects of the anti-CD40 antibody to the tumor. The inhibitory effects that can be determined include, e.g., a decrease of tumor size or tumor volume, a decrease of tumor growth, a reduction of the increase rate of tumor volume in a subject (e.g., as compared to the rate of increase in tumor volume in the same subject prior to treatment or in another subject without such treatment), a decrease in the risk of developing a metastasis or the risk of developing one or more additional metastasis, an increase of survival rate, and an increase of life expectancy, etc. The tumor volume in a subject can be determined by various methods, e.g., as determined by direct measurement, MRI or CT.

In some embodiments, the tumor comprises one or more cancer cells (e.g., human or mouse cancer cells) that are injected into the animal. In some embodiments, the anti-CD40 antibody or anti-CD154 antibody prevents CD154 from binding to CD40. In some embodiments, the anti-CD40 antibody or anti-CD154 antibody does not prevent CD154 from binding to CD40.

In some embodiments, the genetically modified animals can be used for determining whether an anti-CD40 antibody is a CD40 agonist or antagonist. In some embodiments, the methods as described herein are also designed to determine the effects of the agent (e.g., anti-CD40 antibodies) on CD40, e.g., whether the agent can stimulate immune cells or inhibit immune cells (e.g., macrophages, B cells, or DC), whether the agent can increase or decrease the production of cytokines, whether the agent can activate or deactivate immune cells (e.g., macrophages, B cells, or DC), whether the agent can upregulate the immune response or downregulate immune response, and/or whether the agent can induce complement mediated cytotoxicity (CMC) or antibody dependent cellular cytoxicity (ADCC). In some embodiments, the genetically modified animals can be used for determining the effective dosage of a therapeutic agent for treating a disease in the subject, e.g., cancer, or autoimmune diseases.

The inhibitory effects on tumors can also be determined by methods known in the art, e.g., measuring the tumor volume in the animal, and/or determining tumor (volume) inhibition rate (TGI_(TV)). The tumor growth inhibition rate can be calculated using the formula TGI_(TV) (%)=(1−TVt/TVc)×100, where TVt and TVc are the mean tumor volume (or weight) of treated and control groups.

In some embodiments, the anti-CD40 antibody is designed for treating various cancers. As used herein, the term “cancer” refers to cells having the capacity for autonomous growth, i.e., an abnormal state or condition characterized by rapidly proliferating cell growth. The term is meant to include all types of cancerous growths or oncogenic processes, metastatic tissues or malignantly transformed cells, tissues, or organs, irrespective of histopathologic type or stage of invasiveness. The term “tumor” as used herein refers to cancerous cells, e.g., a mass of cancerous cells. Cancers that can be treated or diagnosed using the methods described herein include malignancies of the various organ systems, such as affecting lung, breast, thyroid, lymphoid, gastrointestinal, and genito-urinary tract, as well as adenocarcinomas which include malignancies such as most colon cancers, renal-cell carcinoma, prostate cancer and/or testicular tumors, non-small cell carcinoma of the lung, cancer of the small intestine and cancer of the esophagus. In some embodiments, the agents described herein are designed for treating or diagnosing a carcinoma in a subject. The term “carcinoma” is art recognized and refers to malignancies of epithelial or endocrine tissues including respiratory system carcinomas, gastrointestinal system carcinomas, genitourinary system carcinomas, testicular carcinomas, breast carcinomas, prostatic carcinomas, endocrine system carcinomas, and melanomas. In some embodiments, the cancer is renal carcinoma or melanoma. Exemplary carcinomas include those forming from tissue of the cervix, lung, prostate, breast, head and neck, colon and ovary. The term also includes carcinosarcomas, e.g., which include malignant tumors composed of carcinomatous and sarcomatous tissues. An “adenocarcinoma” refers to a carcinoma derived from glandular tissue or in which the tumor cells form recognizable glandular structures. The term “sarcoma” is art recognized and refers to malignant tumors of mesenchymal derivation.

In some embodiments, the anti-CD40 antibody is designed for treating melanoma (e.g., advanced melanoma), non-small cell lung carcinoma (NSCLC), small cell lung cancer (SCLC), B-cell non-Hodgkin lymphoma, bladder cancer, and/or prostate cancer (e.g., metastatic hormone-refractory prostate cancer). In some embodiments, the anti-CD40 antibody is designed for treating hepatocellular, ovarian, colon, or cervical carcinomas. In some embodiments, the anti-CD40 antibody is designed for treating advanced breast cancer, advanced ovarian cancer, and/or advanced refractory solid tumor. In some embodiments, the anti-CD40 antibody is designed for treating metastatic solid tumors, NSCLC, melanoma, non-Hodgkin lymphoma, colorectal cancer, and multiple myeloma. In some embodiments, the anti-CD40 antibody is designed for treating melanoma, pancreatic carcinoma, mesothelioma, hematological malignancies (e.g., Non-Hodgkin's lymphoma, lymphoma, chronic lymphocytic leukemia), or solid tumors (e.g., advanced solid tumors). In some embodiments, the anti-CD40 antibody is designed for treating carcinomas (e.g., nasopharynx carcinoma, bladder carcinoma, cervix carcinoma, kidney carcinoma or ovary carcinoma).

In some embodiments, the anti-CD40 antibody is designed for treating various autoimmune diseases. Thus, the methods as described herein can be used to determine the effectiveness of an anti-CD40 antibody in inhibiting immune response.

The present disclosure also provides methods of determining toxicity of an antibody (e.g., anti-CD40 antibody). The methods involve administering the antibody to the animal as described herein. The animal is then evaluated for its weight change, red blood cell count, hematocrit, and/or hemoglobin. In some embodiments, the antibody can decrease the red blood cells (RBC), hematocrit, or hemoglobin by more than 20%, 30%, 40%, or 50%. In some embodiments, the animals can have a weight that is at least 5%, 10%, 20%, 30%, or 40% smaller than the weight of the control group (e.g., average weight of the animals that are not treated with the antibody).

The present disclosure also relates to the use of the animal model generated through the methods as described herein in the development of a product related to an immunization processes of human cells, the manufacturing of a human antibody, or the model system for a research in pharmacology, immunology, microbiology and medicine.

In some embodiments, the disclosure provides the use of the animal model generated through the methods as described herein in the production and utilization of an animal experimental disease model of an immunization processes involving human cells, the study on a pathogen, or the development of a new diagnostic strategy and/or a therapeutic strategy.

The disclosure also relates to the use of the animal model generated through the methods as described herein in the screening, verifying, evaluating or studying the CD40 gene function, human CD40 antibodies, drugs for human CD40 targeting sites, the drugs or efficacies for human CD40 targeting sites, the drugs for immune-related diseases and antitumor drugs.

Genetically Modified Animal Model with Two or More Human or Chimeric Genes

The present disclosure further relates to methods for generating genetically modified animal model with two or more human or chimeric genes. The animal can comprise a human or chimeric CD40 gene and a sequence encoding an additional human or chimeric protein.

In some embodiments, the additional human or chimeric protein can be programmed cell death protein 1 (PD-1), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), Lymphocyte Activating 3 (LAG-3), B And T Lymphocyte Associated (BTLA), Programmed Cell Death 1 Ligand 1 (PD-L1), CD27, CD28, CD47, CD137, CD154, T-Cell Immunoreceptor With Ig And ITIM Domains (TIGIT), T-cell

Immunoglobulin and Mucin-Domain Containing-3 (TIM-3), Glucocorticoid-Induced TNFR-Related Protein (GITR), Signal regulatory protein α (SIRPα) or TNF Receptor Superfamily Member 4 (TNFRSF4 or OX40).

The methods of generating genetically modified animal model with two or more human or chimeric genes (e.g., humanized genes) can include the following steps:

(a) using the methods of introducing human CD40 gene or chimeric CD40 gene as described herein to obtain a genetically modified non-human animal;

(b) mating the genetically modified non-human animal with another genetically modified non-human animal, and then screening the progeny to obtain a genetically modified non-human animal with two or more human or chimeric genes.

In some embodiments, in step (b) of the method, the genetically modified animal can be mated with a genetically modified non-human animal with human or chimeric PD-1, CTLA-4, LAG-3, BTLA, PD-L1, CD27, CD28, CD47, CD137, CD154, TIGIT, TIM-3, GITR, SIRPα, or OX40. Some of these genetically modified non-human animal are described, e.g., in PCT/CN2017/090320, PCT/CN2017/099577, PCT/CN2017/099575, PCT/CN2017/099576, PCT/CN2017/099574, PCT/CN2017/106024, PCT/CN2017/110494, PCT/CN2017/110435, PCT/CN2017/120388, PCT/CN2018/081628, PCT/CN2018/081629; each of which is incorporated herein by reference in its entirety.

In some embodiments, the CD40 humanization is directly performed on a genetically modified animal having a human or chimeric PD-1, CTLA-4, BTLA, PD-L1, CD27, CD28, CD47, CD137, CD154, TIGIT, TIM-3, GITR, SIRPα, or OX40 gene.

As these proteins may involve different mechanisms, a combination therapy that targets two or more of these proteins thereof may be a more effective treatment. In fact, many related clinical trials are in progress and have shown a good effect. The genetically modified animal model with two or more human or humanized genes can be used for determining effectiveness of a combination therapy that targets two or more of these proteins, e.g., an anti-CD40 antibody and an additional therapeutic agent for the treatment of cancer. The methods include administering the anti-CD40 antibody and the additional therapeutic agent to the animal, wherein the animal has a tumor; and determining the inhibitory effects of the combined treatment to the tumor. In some embodiments, the additional therapeutic agent is an antibody that specifically binds to PD-1, CTLA-4, BTLA, PD-L1, CD27, CD28, CD47, CD137, CD154, TIGIT, TIM-3, GITR, SIRPa, or OX40. In some embodiments, the additional therapeutic agent is an anti-CTLA4 antibody (e.g., ipilimumab), an anti-PD-1 antibody (e.g., nivolumab), or an anti-PD-L1 antibody.

In some embodiments, the animal further comprises a sequence encoding a human or humanized PD-1, a sequence encoding a human or humanized PD-L1, or a sequence encoding a human or humanized CTLA-4. In some embodiments, the additional therapeutic agent is an anti-PD-1 antibody (e.g., nivolumab, pembrolizumab), an anti-PD-L1 antibody, or an anti-CTLA-4 antibody. In some embodiments, the tumor comprises one or more tumor cells that express CD80, CD86, PD-L1, and/or PD-L2.

In some embodiments, the combination treatment is designed for treating various cancer as described herein, e.g., melanoma, non-small cell lung carcinoma (NSCLC), small cell lung cancer (SCLC), bladder cancer, prostate cancer (e.g., metastatic hormone-refractory prostate cancer), advanced breast cancer, advanced ovarian cancer, and/or advanced refractory solid tumor. In some embodiments, the combination treatment is designed for treating metastatic solid tumors, NSCLC, melanoma, B-cell non-Hodgkin lymphoma, colorectal cancer, and multiple myeloma. In some embodiments, the combination treatment is designed for treating melanoma, carcinomas (e.g., pancreatic carcinoma), mesothelioma, hematological malignancies (e.g., Non-Hodgkin's lymphoma, lymphoma, chronic lymphocytic leukemia), or solid tumors (e.g., advanced solid tumors).

In some embodiments, the methods described herein can be used to evaluate the combination treatment with some other methods. The methods of treating a cancer that can be used alone or in combination with methods described herein, include, e.g., treating the subject with chemotherapy, e.g., campothecin, doxorubicin, cisplatin, carboplatin, procarbazine, mechlorethamine, cyclophosphamide, adriamycin, ifosfamide, melphalan, chlorambucil, bisulfan, nitrosurea, dactinomycin, daunorubicin, bleomycin, plicomycin, mitomycin, etoposide, verampil, podophyllotoxin, tamoxifen, taxol, transplatinum, 5-flurouracil, vincristin, vinblastin, and/or methotrexate. Alternatively or in addition, the methods can include performing surgery on the subject to remove at least a portion of the cancer, e.g., to remove a portion of or all of a tumor(s), from the patient.

EXAMPLES

The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.

Materials and Methods

The following materials were used in the following examples.

C57BL/6 mice were purchased from the China Food and Drugs Research Institute National Rodent Experimental Animal Center.

EcoRI, BamHI, HpaI, SalI, XhoI, KpnI, SpeI, BstBI, ApaI, StuI restriction enzymes were purchased from NEB (Catalog numbers: R3101M, R3136M, R0105S, R3138M, R0146S, R0142S, R3133M, R0159S, R0114S, R0187M).

Ambion in vitro transcription kit was purchased from Ambion (Catalog number: AM1354).

UCA kit was obtained from Beijing Biocytogen Co., Ltd. (Catalog number: BCG-DX-001).

TOP10 competent cells were purchased from the Tiangen Biotech (Beijing) Co. (Catalog number: CB104-02).

Cas9 mRNA was purchased from SIGMA (Catalog number: CAS9MRNA-1EA).

AIO kit was obtained from Beijing Biocytogen Co., Ltd. (Catalog number: BCG-DX-004).

The pHSG299 was purchased from Takara (Catalog number: 3299).

BAC clone library was purchased from Invitrogen (Catalog number: RPCI23.C and RPCI11.C).

Purified NA/LE Hamster Anti-Mouse CD3e (mCD3) antibody was purchased from BD (Catalog number: 553057).

PE anti-mouse CD40 antibody (mCD40PE) was purchased from Biolegend (Catalog number: 124610).

FITC anti-mouse CD19 antibody (mCD19 FITC) was purchased from Biolegend (Catalog number: 115506).

APC anti-human CD40 antibody (hCD40APC) was purchased from Biolegend (Catalog number: 313008).

PerCP/Cy5.5 anti-mouse TCR β chain (mTcR β PerCP) was purchased from Biolegend (Catalog number: 109228).

PE anti-mouse CD279 (PD-1) antibody (mPD-1 PE) was purchased from Biolegend (Catalog number: 109104).

FITC anti-human CD279 (PD-1) antibody (hPD-1 FITC) was purchased from Biolegend (Catalog number: 329904).

Example 1: Design of sgRNA for CD40 Gene

The 5′-terminal targeting sites (sgRNA1 to sgRNA7) and the 3′-terminal targeting sites (sgRNA8 to sgRNA14) were designed and synthesized.

The 5′-terminal targeting sites were located in exon 2 of mouse CD40 gene. The 3′-terminal targeting sites were located in exon 7 of mouse CD40 gene. The targeting site sequences on CD40 for each sgRNA are shown below:

sgRNA-1 target sequence (SEQ ID NO: 1): 5′-gacaaacagtacctccacgatgg-3′ sgRNA-2 target sequence (SEQ ID NO: 2): 5′-cgggacagcttggggtattctgg-3′ sgRNA-3 target sequence (SEQ ID NO: 3): 5′-acgtaacacactgccctagatgg-3′ sgRNA-4 target sequence (SEQ ID NO: 4): 5′-gggtcttggtacggggcaggagg-3′ sgRNA-5 target sequence (SEQ ID NO: 5): 5′-gcatccaccagcaatccaagagg-3′ sgRNA-6 target sequence (SEQ ID NO: 6): 5′-tctcagaccctacacgagtaagg-3′ sgRNA-7 target sequence (SEQ ID NO: 7): 5′-acagactgtgtcacaacccaggg-3′ sgRNA-8 target sequence (SEQ ID NO: 8): 5′-cgcatccgggactttaaacctgg-3′ sgRNA-9 target sequence (SEQ ID NO: 9): 5′-tgaccagcagggctcgcatccgg-3′ sgRNA-10 target sequence (SEQ ID NO: 10): 5′-ccaatggagtgtgctcccactgg-3′ sgRNA-11 target sequence (SEQ ID NO: 11): 5′-actgcttaaaagctctgacctgg-3′ sgRNA-12 target sequence (SEQ ID NO: 12): 5′-tgtgggtaatgtggtcactaggg-3′ sgRNA-13 target sequence (SEQ ID NO: 13): 5′-tggagtgtgctcccactggcagg-3′ sgRNA-14 target sequence (SEQ ID NO: 14): 5′-cattgggagcacccgccagtggg-3′

Example 2: Testing sgRNA Activity

The UCA kit was used to detect the activities of sgRNAs (FIGS. 1A-1B and Table 4). The results show that the guide sgRNAs had different activities. Two of them sgRNA1 (SEQ ID NO: 1) and sgRNA8 (SEQ ID NO: 8) were selected for further experiments.

The synthesized sgRNA sequences based on sgRNA1 and sgRNA8 target sequences are listed in the following table:

TABLE 3 sgRNA1 and sgRNA8 sequences sgRNA1 sequences SEQ ID NO: 15 Upstream: 5′-acaaacagtacctccacga-3′ SEQ ID NO: 16 Downstream: 5′-tcgtggaggtactgtttgt-3′ sgRNA8 sequences SEQ ID NO: 17 Upstream: 5′-catccgggactttaaacc-3′ SEQ ID NO: 18 Downstream: 5′-ggtttaaagtcccggatg-3′

TABLE 4 Activities of sgRNAs 5′-terminal targeting sites 3′-terminal targeting sites Normalized Normalized sgRNAs Activities sgRNAs Activities Negative control 1.00 Negative control (con) 1.00 (con) Positive control (pc) 23.66 Positive control (pc) 41.79 sgRNA-1 14.61 sgRNA-8 39.58 sgRNA-2 17.26 sgRNA-9 21.17 sgRNA-3 4.89 sgRNA-10 7.75 sgRNA-4 13.69 sgRNA-11 7.65 sgRNA-5 10.52 sgRNA-12 3.87 sgRNA-6 1.30 sgRNA-13 5.29 sgRNA-7 14.36 sgRNA-14 18.83

Example 3: Constructing pT7-sgRNA G2 Plasmids

A map of pT7-sgRNA G2 vector is shown in FIG. 2. The plasmid backbone was obtained from Takara (Catalog No. 3299).

The DNA fragment containing T7 promoter and sgRNA scaffold was synthesized, and linked to the backbone vector by restriction enzyme digestion (EcoRI and BamHI) and ligation. The target plasmid was confirmed by the sequencing results.

The DNA fragment containing the T7 promoter and sgRNA scaffold (SEQ ID NO: 19) is shown below:

GAATTCTAATACGACTCACTATAGGGGGTCTTCGAGAAGACCTGTTTTAG AGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAA AGTGGCACCGAGTCGGTGCTTTTAAAGGATCC

Example 4: Constructing Recombinant Expression Vectors pT7-CD40-1 and pT7-CD40-8

TAGG was added to the 5′ end of SEQ ID NO: 15 and SEQ ID NO: 17 to obtain a forward oligonucleotide sequence, and AAAC was added to the 5′ end of the complementary strand (SEQ ID NO: 16 and SEQ ID NO: 18) to obtain a reverse oligonucleotide sequence.

sgRNA-1 forward oligonucleotide: (SEQ ID NO: 59) 5′-TAGGACAAACAGTACCTCCACGA-3′ sgRNA-1 reverse oligonucleotide: (SEQ ID NO: 60) 5′-AAACTCGTGGAGGTACTGTTTGT-3′ sgRNA8 forward oligonucleotide: (SEQ ID NO: 61) 5′-TAGGCATCCGGGACTTTAAACC-3′ sgRNA8 reverse oligonucleotide: (SEQ ID NO: 57) 5′-AAACGGTTTAAAGTCCCGGATG-3′

After annealing, they were respectively ligated to pT7-sgRNA plasmid (linearized with BbsI) to obtain the expression vectors pT7-CD40-1 and pT7-CD40-8. The ligation reaction was set up as follows:

TABLE 5 The ligation reaction mix (10 μL) sgRNA after annealing 1 μL (0.5 μM) pT7-sgRNA G2 vector 1 μL (10 ng) T4 DNA Ligase 1 μL (5U) 10× T4 DNA Ligase buffer 1 μL 50% PEG4000 1 μL H₂O Add to 10 μL

The ligation reaction was carried out at room temperature for 10 to 30 minutes. The ligation product was then transferred to 30 μL of TOP10 competent cells. The cells were then plated on a petri dish with Kanamycin, and then cultured at 37° C. for at least 12 hours and then two clones were selected and added to LB medium with Kanamycin (5 ml), and then cultured at 37° C. at 250 rpm for at least 12 hours.

Clones were randomly selected and sequenced to verify their sequences. The vectors with correct sequences were selected for subsequent experiments.

Example 5: Sequence Design for Humanized CD40

A partial coding sequence of the mouse CD40 gene (Gene ID: 21939) from exons 2-7 (based on the transcript of NCBI accession number NM_011611.2→NP_035741.2 whose mRNA sequence is shown in SEQ ID NO: 20, and the corresponding protein sequence is shown in SEQ ID NO: 21) was replaced with a corresponding coding sequence of human homologous CD40 gene (Gene ID: 958) (based on the transcript of NCBI accession number NM_001250.5→NP_001241.1, whose mRNA sequence was shown in SEQ ID NO: 22, and the corresponding protein sequence is shown in SEQ ID NO: 23). The comparison between the mouse CD40 and human CD40 is shown in FIG. 20, and the finally obtained humanized CD40 gene is shown in FIG. 4. The humanized mouse CD40 gene DNA sequence (chimeric CD40 gene DNA) is shown in SEQ ID NO: 24.

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caggctggagtgcagtggcgcaatctcggctcactgcaagctctgcctcccaggttcacgccattctcctgcctcagcctcc tgagtagctgggactataggcgcccgccaccacacccggctaatttttttgtatttttagtagagacggcgtttcaccgtgt tagccaggatggtcttgatctcctgacctcgtgatccgtctgccttggcctcccaaagtgctgggattacaggcgtgagcca ccgtgcccggccaccagtggtatagtattaatggaatcagtgcattggcttacgtatctgattacagctcagtaagtgtgtg accctcactgagcctcagtctcctcatctgaaaaatgggaatgaccttcatttcacaaggcttgagctaaaaacatgtaaag tgtattgtaaattcctgaatgctctactcatgtaagactaaagtaggccgggcgtggtggctcacacctgtaattgcagcac tttgggaggccgaggagggcagatcatgaggtcaagagatcgagaccatcctggctaatatggtaaaaccctgtctctacta aaaatacaaaaattagctgggcgtggtggcgcacatctgtagtcccagctactcaggaggcggaggcaggagaattgcttga acctgggaggtggaggttgcagtgagctgagatcgcgccactgcattccagccagtctggcgaaagagcaagactctgtctc aaaaaaaaaaaaaaaaaaaaaaaaactaaagtacatggtttcttcaaagcttctctctttctcccaccttagatgatttttc ctttgcaatgtcctgtgtccattccgccccactcctcctggggccacctggaccaggtcttcatcatctcatatctatatgt ttgctgtgtctcctggctggccactcttctgtaatttctcctcctctgagctctctgggcagctgaatcttctcactagtga agtcgcctggttggatgctgatgagactgaccagctgaatccagttgaaaacttcacacttggcagtgatctggttctaaag acacaattttccatagtttcctaacaccatcctgcatgccacctgccttatttccccacatcacatcgtcccacttagcggg actgcactgctgatccaaattttacatcctttagggcccactcaggtcatatgtcctcagggaagtctttctggaagaacct taaaccagaggttctcaacagggggcagttttgctccctgtggaacgtttgccaatgtctggacacatttcattcgtcacac aaacggagagggggatgctacagggatctggcggatagaggccagggatgctgctgaacatctgcaatgcataggacagccc acccccacccccacacccccagtaaataatgatccagcccaagtgtcactggtgctgacgttgagtaaccctatcttaagct gaactcatcatctctccattccagccttggtggattctgtctcctctgaaccattcccatctcactttagcctacctagatc acaaagcttggcactcattatagactcccctatttattactccttcaagatgtgcaagaatcttttctctgcacttttaagt tctgtaagaagagtctgtgtcgttcctataataaccagcataggacgttgcacgtgttgtgtgctcagtgaacctggatttg ttgattgttgactgactcactctagagttggaaatcttatgcttggggaaacttaatatctctttctttctctgtgtgtgtg catttgtgcacgtgtctgtgcatagctgtgagaccaaagacctggttgtgcaacaggcaggcacaaacaagactgatgttgt ctgtggtgagtcctggacaatgggccctggagaaagcctaggaaggtgggaactgaagggggagatgaggcacacaggaaca ctggatgggaaaaaggggaggggaggcagtttgggggtgtggtatcacagctctgccacttatcttgggagtctgggcaaat cacttcccctctcttagcctcagtttcttcatctgtaaaatgggatgataacagcacttccttagtaggttttgattttaga gtgagaaggttggcctacagtaaagatcagataatgtaaatcagtgaaaaaggtcaggggtaagaaaattacattctcttta cctaacgctaaatgaccagttaatgggtgcagcacaccaacatggtacatgtatacatatgtaacaaacctgcacattatgc acatgtaccctaaagcttaaagtataataataataaaatttaaaaaaacgaaaaatacattctctttgctttttctcaaaat gtactttcctctttgtagggctgggactagaatgaggtgagcaaggcacttgccctcgggcgcaatatttaagaaggtgcca taaaagtgtagtaatcaaggtaaattcattttgatgcaatatttttaaaaataaaaattaatgcaaagaaatccatgatgag caagatagcaacattttaaataaagaacaggatccgaccctgtgtttgcatgaccctgcctcactcacctcaccctaatcct ggccctggttccagtaaaaggaataggcagccagcctgcaggccgtagtttgctgacttggtgtccgcctgatgattttcaa aatatggcattaaaagaatgtttaccttgatgactgagtgttttggacatccttttcaattttgtcctgaaacaatttcatc ccttgcctcacgctagtctccgccctgccttttggtctttcttttattttcccactttgaaaaaaaaattcggcatgagaaa tactttacctttcccctccactcttctataccaaaagcaacatgcagacatgaatcatgctagacctcggcattgggcagag agcagggagtggcggggagcatggtgagcaggtggtgacagccactgccaccactcgcttctagatggttcccaggtgggga ggctgccaactggaacccagtcttcccagtttgtaagagaaatcagatgtctaggtttgaatatgtgatctcccagtttaaa aatgtcggcaaatatttccaaacgttaagaaaatgttctggctcctttaaagacatctgccagccacatttccccaaggacc gcggtttgaaccttctgatgtagatgagctctgacattggaagattctggagtctgacaagtcacagcaggttgagggtagg gagaaactgcaggtgaggggtgcatgctgaagtcctgatttctccaggtccccaggatcggctg cgagccctgctggtcatt cctgtcgtgatgggcatcctcatcaccattttcggggtgtttctctatatcagtgagtgctcaggagaggaaagggagggag ggttcagccctgtcgaaccagcctcctgactcaccctcgcaatgtcccacaccccttcttcttctcactagaaaaggtggtc aagaaaccaaaggataatgaggtaagccatccctgagggagagatgctggaaagagtgactggtgggcagggagggaggctc acggcgtagggagacagactcagtaagcagagagctt

SEQ ID NO: 24 shows only the modified portion of DNA sequence, wherein the italicized underlined region is from human CD40.

The coding region sequence, mRNA sequence and the encoded protein sequence thereof of the modified humanized CD40 are respectively shown in SEQ ID NO: 25, SEQ ID NO: 26, and SEQ ID NO: 27.

To the extent that either human CD40 or mouse CD40 has more than one isoforms or transcripts, the methods as described herein can be applied to other isoforms or transcripts.

Example 6: pClon-2G-CD40 Plasmids

Based on the sequences, a targeting strategy for generating the humanized CD40 mouse model is shown in FIG. 3. The 5′ homologous arm comprises nucleic acid 165060750-165062291 of NCBI Accession No. NC_000068.7 (SEQ ID NO: 28). The 3′ homologous arm comprises nucleic acid 165069646-165071120 of NCBI Accession No. NC_000068.7 (SEQ ID NO: 29). The human sequence corresponds to 46121826-46128154 of NCBI Accession No. NC_000020.11 (SEQ ID NO: 30).

Primers for amplifying the 5 recombination fragments (LR, A1, A2, A3, RR) and related sequences were designed. Among them, the LR fragment corresponds to the 5′ homologous arm, the RR fragment corresponds to the 3′ homologous arm, the A1+A2+A3 fragments correspond to the human CD40 sequence.

The primers are shown in the table below.

TABLE 6 Primers for recombination fragments Fragment Length (bp) Primer sequence LR 1575 bp F: 5′-ctagctcgagctgctggacaaacctcagagagtggctgc-3′ (SEQ ID NO: 31) R: 5′-ctgcatgcagtgggtggttctggatggacctaaaaacagaagtggacagc-3′ (SEQ ID NO: 32) A1 1425 bp F: 5′-gctgtccacttctgtttttaggtccatccagaaccacccactgcatgcagag-3′ (SEQ ID NO: 33) R: 5′-ctagggtaccatcgactagtatctttcgaaagcagatgacacattgg-3′ (SEQ ID NO: 34) A2 2627 bp F: 5′-ccaatgtgtcatctgctttcgaaaaatg-3′ (SEQ ID NO: 35) R: 5′-ggcgacttcactagtgagaagattcag-3′ (SEQ ID NO: 36) A3 2401 bp F: ctgaatcttctcactagtgaatcgcc-3′ (SEQ ID NO: 37) R: 5′-acaggaatgaccagcagggctcgcagccgatcctggggacctggag-3′ (SEQ ID NO: 38) RR 1507 bp F: 5′-tccaggtccccaggatcggctgcgagccctgctggtcattcctgtc-3′ (SEQ ID NO: 39) R: 5′-ctagggtaccttggtaggtatcactgtggaccccc-3′ (SEQ ID NO: 40)

KOD-plus DNA polymerase was used to amplify the recombination fragments from Bacterial Artificial Chromosome (BAC) clones. Among them, BAC clones with mouse CD40 (Catalog number: RP23-89H6) were used as a template for LR and RR recombination fragments, and BAC clones with human CD40 (Catalog number: RP11-177B15) were used as a template for A1, A2, and A3 recombination fragments. The conditions for the PCR amplification were shown in the tables below.

TABLE 7 The PCR reaction system (20 μL) Composition Amount 10× buffer for KOD-plus DNA polymerase 2 μl dNTP (2 mM) 2 μL MgSO₄ (25 mM) 0.8 μL Upstream primer F (10 μM) 0.6 μL Downstream primer R (10 μM) 0.6 μL BAC DNA templates 50 ng KOD-Plus DNA polymerase (1 U/μL) 0.6 μL H₂O Add to 20 μL

TABLE 8 The PCR reaction conditions Temperature Time Cycles 94° C.  5 min 1 94° C. 30 sec 15 67° C. (−0.7° C./cycle) 30 sec 68° C.  1 kb/min 94° C. 30 sec 25 57° C. 30 sec 68° C.  1 kb/min 68° C. 10 min 1  4° C. 10 min 1

The PCR products (DNA fragments) LR, A1, A2, A3, and RR were collected and were used to construct targeting vectors. The targeting vectors were obtained by the following steps:

-   (1). Fragments LR and A1 were ligated by overlap PCR (Phusion DNA     Polymerases). Fragment A3 and RR were also ligated by overlap PCR.     The conditions for ligation were shown in the tables below. The     sequences of LR-A1 and A3-RR were verified by sequencing. -   (2). Fragments were ligated to the pClon-2G plasmid in the AIO kit     by restriction enzymes in the following order: LR-A1 (XhoI+KpnI),     A3-RR (SpeI+KpnI), A2 (BstBI+SpeI) to obtain pClon-2G-CD40 vector.

TABLE 9 The PCR reaction system (20 μL) Composition Amount 5× Phusion HF Buffer 4 μL dNTP (10 mM) 0.4 μL Primer F (10 μM) 1 μL Primer R (10 μM) 1 μL DNA template 5 ng Phusion DNA polymerase (2 U/μL) 0.2 μL H₂O Add to 20 μL

TABLE 10 The PCR reaction conditions Temperature Time Cycles 98° C. 30 sec 1 98° C. 10 sec 35 58° C. 25 sec 72° C. 30 sec/kb 72° C. 5-10 min 1  4° C. 10 min 1

When fragments LR and A1 were ligated, Primer F in Table 9 was SEQ ID NO: 31, Primer R was SEQ ID NO: 34, and the DNA template was the recovered PCR amplification product of the LR fragment and A1 fragment. When fragments A3 and RR were ligated, Primer F was SEQ ID NO: 37, primer R was SEQ ID NO: 40, and the DNA template was the recovered PCR amplification product of the A3 fragment and RR fragment.

Example 7. Verification of pClon-2G-CD40 Vectors

Two pClon-2G-CD40 clones were randomly selected and tested by three sets of restriction enzymes. Among them, HpaI+SalI should generate 839 bp+2608 bp+3578 bp+5072 bp fragments; ApaI+XhoI should generate 1203 bp+1985 bp+2532 bp+6377 bp fragments; EcoRI+StuI should generate 201 bp+398 bp+1825 bp+9673 bp fragments. Plasmids 2 and 3 had the expected results (FIG. 5). The sequences of Plasmid 3 were further confirmed by sequencing.

Example 8: Microinjection and Embryo Transfer Using C57BL/6 Mice

The pre-mixed Cas9 mRNA, pClon-2G-CD40 plasmid and in vitro transcription products of pT7-CD40-1, pT7-CD40-8 plasmids were injected into the cytoplasm or nucleus of mouse fertilized eggs (C57BL/6 background) with a microinjection instrument (using Ambion in vitro transcription kit to carry out the transcription according to the method provided in the product instruction). The embryo microinjection was carried out according to the method described, e.g., in A. Nagy, et al., “Manipulating the Mouse Embryo: A Laboratory Manual (Third Edition),” Cold Spring Harbor Laboratory Press, 2003. The injected fertilized eggs were then transferred to a culture medium for a short time culture, and then was transplanted into the oviduct of the recipient mouse to produce the genetically modified humanized mice (F0 generation). The mouse population was further expanded by cross-mating and self-mating to establish stable mouse lines. These humanized mice were named as B-hCD40.

Example 9: Verification of Genetic Modification 1. Genotype Determination for F0 Generation Mice

PCR analysis was performed using mouse tail genomic DNA of F0 generation mice. Primer L-GT-F is located on the left side of 5′ homologous arm, Primer R-GT-R is located on the right side of 3′ homologous arm, and both R-GT-F and L-GT-R are located within the fifth intron.

5′ end primers: Upstream: L-GT-F (SEQ ID NO: 41) 5′-GAAGTGTTACAGCTCCGCTCTGAGG-3′; Downstream: L-GT-R (SEQ ID NO: 42) 5′-AGCTCAAGCCTTGTGAAATGAAGGT-3′ 3′ end primers: Upstream: R-GT-F (SEQ ID NO: 43) 5′-AATGGAATCAGTGCATTGGCTTACG-3′; Downstream: R-GT-R (SEQ ID NO: 44) 5′-TTTGGGCAGCAAGCTCCTTTACTCA-3′

If the desired human sequence was inserted into the correct positions in the genome, PCR experiments using the above primers should generate only one band. The 5′ end PCR experiment should produce a band at about 5050 bp, and the 3′ end PCR experiment should produce a band at about 4832 bp. The results for F0 generation mice are shown in FIGS. 6A-6B.

TABLE 11 The PCR reaction (20 μL) 10× buffer 2 μL dNTP (2 mM) 2 μL MgSO₄ (25 mM) 0.8 μL Upstream primer (10 μM) 0.6 μL Downstream primer (10 μM) 0.6 μL Mouse tail genomic DNA 200 ng KOD-Plus-(1 U/μL) 0.6 μL ddH₂O Add to 20 μL

TABLE 12 The PCR reaction conditions Temperature Time Cycles 94° C.  5 min 1 94° C. 30 sec 15 67° C. (−0.7° C./cycle) 30 sec 68° C.  1 kb/min 94° C. 10 sec 25 56° C. 30 sec 68° C.  1 kb/min 68° C. 10 min 1  4° C. 10 min 1

2. Expression Level Analysis in Humanized Mice

One humanized F1 heterozygous mouse was selected. One wildtype mouse in the same background was used as the control.

7.5 μg of anti-mCD3 antibody was injected intraperitoneally to the mice. The spleens were collected 24 hours after the injection, and the spleen samples were grinded. The samples were then passed through 70 μm cell mesh. The filtered cell suspensions were centrifuged and the supernatants were discarded. Erythrocyte lysis solution was added to the sample, which was lysed for 5 min and neutralized with PBS solution. The solution was centrifuged again and the supernatants were discarded. The cells were washed with PBS and tested in FACS.

Flow cytometry was performed with wildtype mice and F1 generation humanized CD40 mice (FIG. 7). In the control groups, no spleen cells stained with hCD40 APC were observed; in humanized CD40 groups, spleen cells stained with hCD40 APC were observed in heterozygous humanized CD40 mice.

The F1 generation humanized CD40 heterozygotes with the same background were mated with each other to produce humanized CD40 homozygotes. The same experiments described above were performed on these humanized CD40 homozygous mice.

One humanized CD40 homozygous mouse (7 weeks old) was selected. Two wildtype mice in the same background was used as the controls.

7.5 μg of anti-mCD3 antibody was injected intraperitoneally to the mice. The spleens were collected 24 hours after the injection, and the spleen samples were grinded. The samples were then passed through 70 μm cell mesh. The filtered cell suspensions were centrifuged and the supernatants were discarded. Erythrocyte lysis solution was added to the sample, which was lysed for 5 min and neutralized with PBS solution.

FACS was performed. The results were shown in FIGS. 8A-8F. In the control groups, no spleen cells stained with hCD40 APC were detected (FIGS. 8D and 8E); in contrast, spleen cells stained with hCD40 APC were observed in homozygous humanized CD40 mice (FIG. 8F).

Example 10: CD40 Knockout Mice

Since the cleavage of Cas9 results in DNA double strands break, and the homologous recombination repair may result in insertion/deletion mutations, it is possible to obtain CD40 knockout mice by the methods described herein. A pair of primers was thus designed to target the left side of the 5′ target site and the right side of the 3′ target site:

F: (SEQ ID NO: 45) 5′-GCATCAAGCTTGGTACCGATGTTCTGCGTTCTTGCTTTGGTAGAT G-3′ R: (SEQ ID NO: 46) 5′-ACTTAATCGTGGAGGATGATCTCATTATCCTTTGGTTTCTTGACC ACC-3′

For wildtype mice, there should be no PCR band, and there should be only one band (about 500 bp) for CD40 knockout mice.

The PCR reaction systems and conditions are shown in the tables below.

TABLE 13 2× PCR buffer 10 μL dNTP (2 mM) 4 μL Upstream primer (10 μM) 0.6 μL Downstream primer (10 μM) 0.6 μL Genomic DNA from mouse tail 100 ng KOD-FX (1 U/μL) 0.4 μL H₂O Add to 20 μL

TABLE 14 Temperature Duration Cycles 94° C.  5 min 1 98° C. 30 sec 35 62° C. 30 sec 68° C. 30 sec 68° C. 10 min 1  4° C. 10 min 1

FIG. 9 shows the PCR results. KO-1 and KO-11 were CD40 knockout mice.

Example 11. Pharmacological Validation of B-hCD40 Humanized Animal Model

B-hCD40 heterozygous mice (4 weeks) were subcutaneously injected with mouse colon cancer cell MC38 (5×10⁵/100 μl PBS), and when the tumor volume grew to about 100 mm³, the mice were divided to a control group and six treatment groups based on tumor size (n=5/group). The treatment groups were randomly selected for anti-human CD40 antibodies (AB1, AB2, AB3, AB4, AB5, AB6) treatment (3 mg/kg); the control group was injected with an equal volume of blank solvent. The frequency of administration was twice a week (6 times of administrations in total). The tumor volume was measured twice a week and the body weight of the mice was weighed as well. Euthanasia was performed when the tumor volume of the mouse reached 3000 mm³. The tested antibodies were generated by immunizing mice with human CD40 proteins. A detailed description of these methods can be found in Murphy, et al., Janeway's immunobiology. Garland Science, 2016 (9^(th) edition), which is incorporated herein by reference in its entirety.

Overall, the animals in each group were healthy, and the body weights of all the treatment and control group mice increased, and were not significantly different from each other (FIGS. 10 and 11). The tumor in the control group continued growing during the experimental period (FIG. 12); when compared with the control group mice, the tumor volumes in the treatment groups were smaller than the control group (FIG. 12). Thus, the anti-CD40 antibodies were well tolerated, and the antibodies inhibited the tumor growth in mice.

Table 15 shows results for this experiment, including the tumor volumes at the day of grouping, 14 days after the grouping, and at the end of the experiment (day 25), the survival rate of the mice, the Tumor Growth Inhibition value (TGI_(TV)), and the statistical differences (P value) in mouse body weights and tumor volume between the treatment and control groups.

TABLE 15 P value Tumor volume (mm³) Body Tumor Day 0 Day 14 Day 25 Survival TGI_(TV) % weight Volume Control G1 123 ± 10 819 ± 187 2677 ± 844 5/5 N/A N/A N/A Treatment G2(AB1) 124 ± 14 699 ± 119 2460 ± 387 5/5 8.5 0.610 0.821 groups G3(AB2) 121 ± 10 634 ± 211 2424 ± 754 5/5 9.8 0.719 0.829 G4(AB3) 121 ± 14 481 ± 124 1124 ± 247 5/5 60.7 0.636 0.115 G5(AB4) 121 ± 9 748 ± 80 2121 ± 254 5/5 21.7 0.888 0.546 G6(AB5) 122 ± 11 472 ± 161 1522 ± 411 5/5 45.2 0.553 0.254 G7(AB6) 122 ± 15 643 ± 100 1954 ± 333 5/5 28.3 0.969 0.449

At the end of the experiment (day 25), the body weight of each group increased and there was no significant difference between the groups (p>0.05), indicating that the animals tolerated the six anti-hCD40 antibodies well. With respect to the tumor volume, in the control group (G1), the average tumor volume was 2677±844 mm³. The average tumor volumes in the treatment groups were 2460±387 mm³ (G2), 2424±754 mm³ (G3), 1124±247 mm³ (G4), 2121±254 mm³ (G5), 1522±411 mm³ (G6), and 1954±333 mm³ (G7).

The tumor volumes in all treatment groups (G2-G7) were smaller than those in the control group (G1). The results show that anti-human CD40 antibody AB1, AB2, AB3, AB4, AB5, AB6 had different tumor inhibitory effects in B-hCD40 mice. Under the same condition, the inhibitory effects of AB3 (G4) were better than other CD40 antibodies (>60%). These antibodies had no obvious toxic effects in mice.

In another experiment, three additional anti-hCD40 antibodies (AB7, AB8, and AB9) were tested in B-hCD40 homozygous mice. The methods were the same as described above. The body weight of mice and the percentage changes during the experimental period are shown in FIGS. 13 and 14. The results of tumor volumes are shown in FIG. 15. The results of the experiments are also summarized in the table below.

TABLE 16 P value Tumor volume (mm³) Body Tumor Day 0 Day 14 Day 21 Survival TGI_(TV) % weight Volume Control G1 126 ± 5 1014 ± 142 2779 ± 425 5/5 N/A N/A N/A Treatment G2(AB7) 125 ± 7 1121 ± 171 26780 ± 453  5/5 3.62 0.97 0.875 groups G3(AB8) 125 ± 7  938 ± 165 1759 ± 340 5/5 36.7 0.76 0.098 G4(AB9) 125 ± 7 583 ± 60 1107 ± 153 5/5 60.7 0.74 0.006

The above examples have demonstrated that the B-hCD40 mouse model can be used as an in vivo animal model for screening, evaluating human CD40 signaling pathway regulators, and testing the efficacy of multiple anti-human CD40 antibodies.

Example 12: Mice with Two or More Humanized Genes

Mice with the humanized CD40 gene (e.g., animal model with humanized CD40 prepared using the methods as described in the present disclosure) can also be used to prepare an animal model with double-humanized or multi-humanized genes. For example, in Example 8, the embryonic stem cell used in the microinjection and embryo transfer process can be selected from the embryos of other genetically modified mice, so as to obtain double- or multiple-gene modified mouse models. The fertilized eggs of B-hCD40 mice can also be further genetically engineered to produce mouse lines with one or more humanized or otherwise genetically modified mouse models. In addition, the humanized CD40 animal model homozygote or heterozygote can be mated with other genetically modified homozygous or heterozygous animal models (or through IVF), and the progeny can be screened. According to the Mendelian law, there is a chance to obtain the double-gene or multiple-gene modified heterozygous animals, and then the heterozygous animals can be mated with each other to finally obtain the double-gene or multiple-gene modified homozygotes.

In the case of generating double humanized CD40/PD-1 mice, since the mouse CD40 gene and PD-1 gene are located on different chromosomes, the double humanized CD40/PD-1 mouse model was obtained by crossing the CD40 humanized mice with PD-1 humanized mice (e.g., B-hPD-1 mice).

PCR analysis was performed on the genomic DNA collected from mouse tails of double humanized CD40/PD-1 mice. Four pairs of primers were used. The specific sequences, the product lengths, the reaction conditions are shown in the tables below. The results for a number of humanized CD40/PD-1 mice are shown in FIGS. 16A-16D, wherein FIGS. 16A and 16B show that the mice numbered 178, 183, 186, and 187 were homozygous for humanized CD40. Mice numbered 179, 180, 184, 185, 189, 190, 192, and 193 were heterozygous for humanized CD40. FIGS. 16C and 16D show that the mice numbered 178, 185, 186, 190, and 192 were homozygous for humanized PD-1, and mice numbered 179, 180, 182, 187, 188, 189 and 191 were heterozygous for humanized PD-1. The results show that the mice numbered 178 and 186 were homozygous for both humanized CD40 and humanized PD-1 (CD40^(H/H)/PD-1^(H/H)). Mice numbered 179, 180, and 189 were heterozygous for both humanized CD40 and humanized PD-1 (CD40^(H/+)/PD-1^(H/+)).

TABLE 17 Primer sequences Product Primer Sequence length CD40 WT F: 5′-acatgccggtggaagatccc-3′ (SEQ ID NO: 47) WT: 278 bp R: 5′-gagacgggacagcttggggt-3′ (SEQ ID NO: 48) CD40 MUT F: 5′-agacatctgccagccacatttccc-3′ (SEQ ID NO: 49) Mut: 381 bp R: 5′-ctcattatcctttggtttcttgaccacc-3′ (SEQ ID NO: 50 PD-1 MUT F: 5′-cttccacatgagcgtggtcagggcc-3′ (SEQ ID NO: 51) Mut: 325 bp R: 5′-ccaagggactattttagatgggcag-3′ (SEQ ID NO: 52) PD-1 WT F: 5′-gaagctacaagctcctaggtaggggg-3′ (SEQ ID NO: 53) WT: 345 bp R: 5′-acgggttggctcaaaccattaca-3′ (SEQ ID NO: 54)

TABLE 18 PCR reaction system Composition Volume 2x Master Mix 10 μL Upstream primer (10 μM) 0.5 μL Downstream primer (10 μM) 0.5 μL Mouse tail genomic DNA (100-200 ng/20 ml) 2 μL ddH₂O Add to 20 μL

TABLE 19 PCR amplification reaction condition Temperature Time Cycles 95° C.  5 min 1 95° C. 30 sec 30 59° C. 30 sec 72° C. 30 sec 72° C. 10 min 1  4° C. 10 min 1

Protein expression in the double humanized CD40/PD-1 mice was further examined. A double humanized CD40/PD-1 homozygote was selected for the study. As shown in FIGS. 17A-17F and FIGS. 18A-18F, anti-hCD40 APC and anti-hPD-1 FITC antibodies detected the expression of humanized CD40 and humanized PD-1 on the spleen cells of the double humanized CD40/PD-1 homozygous mouse (FIGS. 17F and 18F). Anti-hCD40 APC and anti-hPD-1 FITC antibodies did not detect the expression of humanized CD40 or humanized PD-1 on the spleen cells of the wildtype mice.

Example 13: Double Humanized CD40/PD-L1 Mice

Since the mouse CD40 gene is located on chromosome 2 and PD-L1 gene is located on chromosome 19, the double humanized CD40/PD-L1 mouse model was obtained by crossing the CD40 humanized mice with PD-L1 humanized mice.

PCR analysis was performed on the genomic DNA collected from mouse tails of double humanized CD40/PD-L1 mice. Four pairs of primers were used. The specific sequences, the product lengths, and the reaction conditions are shown in tables below. The results for a number of humanized CD40/PD-L1 mice are shown in FIGS. 19A-19D. FIGS. 19A and 19B show that the mice numbered 1-20 were heterozygous for humanized CD40. FIGS. 19C and 19D show that the mice numbered 1-20 were homozygous for humanized PD-L1. Thus, the mice numbered 1-20 were CD40^(H/+)/PD-L1^(H/H) mice.

TABLE 20 Primer sequences Product Primer Sequence length CD40 WT F: (SEQ ID NO: 47) WT: 278 bp R: (SEQ ID NO: 48) CD40 MUT F: (SEQ ID NO: 49) Mut: 381 bp R: (SEQ ID NO: 50) PD-L1 MUT F: 5′-ccagggaggtggcccactgataata-3′ (SEQ ID NO: 55) Mut: 528 bp R: 5′-actaacgcaagcaggtccagctccc-3′ (SEQ ID NO: 56) PD-L1 WT F: 5′-ccagggaggtggcccactgataata-3′ (SEQ ID NO: 55) WT: 356 bp R: 5′-cacccctgcatcctgcaatttcaca-3′ (SEQ ID NO: 58)

Example 14. Methods Based on Embryonic Stem Cell Technologies

The non-human mammals described herein can also be prepared through other gene editing systems and approaches, including but not limited to: gene homologous recombination techniques based on embryonic stem cells (ES), zinc finger nuclease (ZFN) techniques, transcriptional activator-like effector factor nuclease (TALEN) technique, homing endonuclease (megakable base ribozyme), or other techniques.

Based on the CD40 transcript and the corresponding protein sequence and the humanized CD40 mouse gene map as shown in FIG. 4, a targeting strategy for generating the humanized CD40 mouse model with Embryonic Stem Cell Technologies is developed (FIG. 21). Since the objective is to replace exons 2-7 of the mouse CD40 gene in whole or in part with the corresponding sequence in human CD40 gene, a recombinant vector that contains a 5′ homologous arm (4719 bp), a 3′ homologous arm (4184 bp) and sequence fragment from human CD40 (total 6329 bp) is designed. The vector can also contain a resistance gene for positive clone screening, such as neomycin phosphotransferase coding sequence Neo. On both sides of the resistance gene, two site-specific recombination systems in the same orientation, such as Frt or LoxP, can be added. Furthermore, a coding gene with a negative screening marker, such as the diphtheria toxin A subunit coding gene (DTA), can be constructed downstream of the recombinant vector 3′ homologous arm.

Vector construction can be carried out using methods known in the art, such as enzyme digestion and so on. The recombinant vector with correct sequence can be next transfected into mouse embryonic stem cells, such as C57BL/6 mouse embryonic stem cells, and then the recombinant vector can be screened by positive clone screening gene. The cells transfected with the recombinant vector are next screened by using the positive clone marker gene, and Southern Blot technique can be used for DNA recombination identification. For the selected correct positive clones, the positive clonal cells (black mice) are injected into the isolated blastocysts (white mice) by microinjection according to the method described in the book A. Nagy, et al., “Manipulating the Mouse Embryo: A Laboratory Manual (Third Edition),” Cold Spring Harbor Laboratory Press, 2003. The resulting chimeric blastocysts formed following the injection are transferred to the culture medium for a short time culture and then transplanted into the fallopian tubes of the recipient mice (white mice) to produce F0 generation chimeric mice (black and white). The F0 generation chimeric mice with correct gene recombination are then selected by extracting the mouse tail genome and detecting by PCR for subsequent breeding and identification. The F1 generation mice are obtained by mating the F0 generation chimeric mice with wildtype mice. Stable gene recombination positive F1 heterozygous mice are selected by extracting rat tail genome and PCR detection. Next, the F1 heterozygous mice are mated to each other to obtain genetically recombinant positive F2 generation homozygous mice. In addition, the F1 heterozygous mice can also be mated with Flp or Cre mice to remove the positive clone screening marker gene (e.g., neo), and then the CD40 gene humanized homozygous mice can be obtained by mating these mice with each other. The methods of genotyping and using the F1 heterozygous mice or F2 homozygous mice are similar to the methods as described in the examples above.

OTHER EMBODIMENTS

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. 

1. A genetically-modified, non-human animal whose genome comprises at least one chromosome comprising a sequence encoding a human or chimeric CD40.
 2. The animal of claim 1, wherein the sequence encoding the human or chimeric CD40 is operably linked to an endogenous regulatory element at the endogenous CD40 gene locus in the at least one chromosome.
 3. The animal of claim 1, wherein the sequence encoding a human or chimeric CD40 comprises a sequence encoding an amino acid sequence that is at least 70% identical to SEQ ID NO:
 23. 4. The animal of claim 1, wherein the sequence encoding a human or chimeric CD40 comprises a sequence encoding an amino acid sequence that is at least 70% identical to SEQ ID NO:
 27. 5. The animal of claim 1, wherein the human or chimeric CD40 comprises a sequence that is at least 90% identical to amino acids 20-192 of SEQ ID NO:
 23. 6. The animal of claim 1, wherein the animal is a rodent.
 7. The animal of claim 1, wherein the animal is a mouse.
 8. The animal of claim 1, wherein the animal does not express endogenous CD40.
 9. The animal of claim 1, wherein the animal has one or more cells expressing human or chimeric CD40. 10.-11. (canceled)
 12. A genetically-modified, non-human animal, wherein the genome of the animal comprises a replacement of a sequence encoding a region of endogenous CD40 with a sequence encoding a corresponding region of human CD40 at an endogenous CD40 gene locus. 13.-14. (canceled)
 15. The animal of claim 12, wherein the replaced locus is the extracellular region of CD40.
 16. The animal of claim 12, wherein the animal has one or more cells expressing a chimeric CD40 having an extracellular region, a transmembrane region, and a cytoplasmic region, wherein the extracellular region comprises a sequence that is at least 70% identical to the extracellular region of human CD40. 17.-19. (canceled)
 20. The animal of claim 12, wherein the animal is homozygous with respect to the replacement at the endogenous CD40 gene locus.
 21. A method for making a genetically-modified, non-human animal, comprising: replacing in at least one cell of the animal, at an endogenous CD40 gene locus, a sequence encoding a region of an endogenous CD40 with a sequence encoding a corresponding region of human CD40.
 22. The method of claim 21, wherein the sequence encoding the corresponding region of human CD40 comprises exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, exon 7, exon 8, and/or exon 9 of a human CD40 gene. 23.-24. (canceled)
 25. The method of claim 21, wherein the region is located within the extracellular region of CD40. 26.-36. (canceled)
 37. The animal of claim 1, wherein the animal further comprises a sequence encoding an additional human or chimeric protein.
 38. The animal of claim 37, wherein the additional human or chimeric protein is programmed cell death protein 1 (PD-1), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), Lymphocyte Activating 3 (LAG-3), B And T Lymphocyte Associated (BTLA), Programmed Cell Death 1 Ligand 1 (PD-L1), CD27, CD28, CD47, CD137, CD154, T-Cell Immunoreceptor With Ig And ITIM Domains (TIGIT), T-cell Immunoglobulin and Mucin-Domain Containing-3 (TIM-3), Glucocorticoid-Induced TNFR-Related Protein (GITR), Signal regulatory protein α (SIRPα) or TNF Receptor Superfamily Member 4 (OX40). 39.-40. (canceled)
 41. A method of determining effectiveness of an anti-CD40 antibody for the treatment of cancer, comprising: administering the anti-CD40 antibody to the animal of claim 1, wherein the animal has a tumor; and determining the inhibitory effects of the anti-CD40 antibody to the tumor.
 42. (canceled)
 43. The method of claim 41, wherein the tumor comprises one or more human cancer cells that are injected into the animal. 44.-57. (canceled) 